R/plot_radial.R
In WSpiller/MRPracticals: An R Package illustrating features of MR Base and RadialMR
Defines functions
plot_radial
Documented in
plot_radial
#' plot_radial
#'
#' A function for producing radial IVW and MR-Egger plots either individually or simultaneously. The function allows for a variety of aesthetic and scaling options, utilising the output from the \code{IVW_radial} and \code{egger_radial} functions.
#'
#' @param r_object An object of class \code{"IVW"} or \code{"egger"}. For visualising both estimates simultaneously, both objects should be included as a vector c(\code{A},\code{B}), where \code{A} and \code{B} denote the \code{"IVW"} and \code{"egger"} objects respectively.
#' @param radial_scale Indicates whether to produce a plot including a full radial scale (\code{TRUE}), or a scatterplot showing only the effect estimates (\code{FALSE}).
#' @param show_outliers Indicates whether display only the set of variants identified as outliers (\code{TRUE}) or the complete set of variants (\code{FALSE}). Note that when (\code{show_outliers=TRUE}), non-outlying variants further from the origin than the furthest outlier will cause an error message that one or more points have been omitted. These are non-outlying variants beyond the scale. If no outliers are present, a plot will be produced using the full set of variants, with an accompanying message indicating the absence of outliers.
#' @param scale_match Indicates whether x and y axes should have the same range(\code{TRUE}), or different ranges (\code{FALSE}) This improves the interpretation of the radial scale, and is set to \code{FALSE} when the radial scale is omitted from the plot.
#' @return A ggplot object containing a radial plot of either the IVW, MR-Egger, or both estimates simultaneously.
#'@author Wes Spiller; Jack Bowden.
#'@references Bowden, J., et al., Improving the visualization, interpretation and analysis of two-sample summary data Mendelian randomization via the Radial plot and Radial regression. International Journal of Epidemiology, 2018. 47(4): p. 1264-1278.
#'@export
#'@examples
#'
#'plot_radial(r_object,TRUE,TRUE,TRUE)
#'
#'plot_radial(c(r_object,r_object),TRUE,TRUE,FALSE)
plot_radial<-function(r_object,radial_scale,show_outliers,scale_match){
if(missing(radial_scale)) {
radial_scale<-T
}
if(missing(show_outliers)) {
show_outliers<-F
}
if(missing(scale_match)) {
scale_match<-T
}
#Load ggplot2 library
library(ggplot2)
#Function for producing scale and confidence interval circle indicators
circle.radial <- function(center = c(0,0), radius, num.points, START,END){
R = radius
tt <- seq(START,END,length.out = num.points)
#Generates x-axis values for circle
xx <- center[1] + R * cos(tt)
#Generates y-axis values for circle
yy <- center[2] + R * sin(tt)
return(data.frame(x = xx, y = yy))
}
if(length(r_object)>=6 && length(r_object)<=13){
if(class(r_object)=="IVW"){
r_object$coef<-c(r_object$coef[2,])
r_object$coef<-as.numeric(r_object$coef)
#Define radius for scale and IVW circles
maximal<-atan(max(abs(r_object$data[,3]))/max(r_object$data[,2]))
R.All<-max(abs(r_object$data[,3]))/sin(maximal)
R.IVW<-R.All+(R.All/12)
#Define scaling parameter
Label.Scaling<-R.IVW/24
Scalemin<-min(r_object$data[,3]/r_object$data[,2],r_object$confint[1])
Scalemax<-max(r_object$data[,3]/r_object$data[,2],r_object$confint[2])
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
#Plot circle for IVW estimate
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Function for rounding to nearest 0.05 increment
mround <- function(x){
0.5*round(x/0.5)
}
#If only outliers are to be shown
if(show_outliers==TRUE){
#If the full scale is to be shown
if(radial_scale==TRUE){
#If axes scales should be fixed
if(scale_match==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Redefine scale and IVW circle radii
maximal<-atan(max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$Wj)))
R.All<-max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/sin(maximal)
R.IVW<-R.All+(R.All/12)
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
#Plot circle for IVW estimate
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate plot showing only outliers using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Outlier","IVW"),values=c("#56B4E9","#E69F00","white"))
#Function for rounding to nearest 0.05 increment
mround <- function(x){
0.5*round(x/0.5)
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw individual ratio estimate lines for each outlier and Q distance indicator lines
Theta<-rep(0,length(r_object$data[r_object$data$Outliers == "Outlier", ]$Outliers))
for(i in 1:length(r_object$data[r_object$data$Outliers == "Outlier", ][,3])){
Theta<-atan(r_object$data[r_object$data$Outliers == "Outlier", ][,3]/r_object$data[r_object$data$Outliers == "Outlier", ][,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
B<- B + geom_segment(x = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], xend = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i],
y = r_object$data[r_object$data$Outliers == "Outlier", ][,3][i], yend =r_object$data[r_object$data$Outliers == "Outlier", ][,2][i]*
r_object$coef[1],linetype="solid",colour="#56B4E9")
}
}
}
#If axes scales should be fixed
if(scale_match==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Redefine scale and IVW circle radii
maximal<-atan(max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$Wj)))
R.All<-max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/sin(maximal)
R.IVW<-R.All+(R.All/12)
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
#Plot circle for IVW estimate
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate plot showing only outliers using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Outlier","IVW"),values=c("#56B4E9","#E69F00","white"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw individual ratio estimate lines for each outlier and Q distance indicator lines
Theta<-rep(0,length(r_object$data[r_object$data$Outliers == "Outlier", ]$Outliers))
for(i in 1:length(r_object$data[r_object$data$Outliers == "Outlier", ][,3])){
Theta<-atan(r_object$data[r_object$data$Outliers == "Outlier", ][,3]/r_object$data[r_object$data$Outliers == "Outlier", ][,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
B<- B + geom_segment(x = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], xend = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i],
y = r_object$data[r_object$data$Outliers == "Outlier", ][,3][i], yend =r_object$data[r_object$data$Outliers == "Outlier", ][,2][i]*
r_object$coef[1],linetype="solid",colour="#56B4E9")
}
}
}
}
#If the full scale is to be shown
if(radial_scale==FALSE){
#If axes scales should be fixed
if(scale_match==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Redefine scale and IVW circle radii
maximal<-atan(max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$Wj)))
R.All<-max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/sin(maximal)
R.IVW<-R.All+(R.All/12)
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
#Plot circle for IVW estimate
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate plot showing only outliers using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Outlier","IVW"),values=c("#56B4E9","#E69F00","white"))
#Draw lines indicating individual Q contributions and give text displaying each value
for(i in 1:length(r_object$data[r_object$data$Outliers == "Outlier", ][,3])){
B<- B + geom_segment(x = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], xend = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], y = r_object$data[r_object$data$Outliers == "Outlier", ][,3][i], yend =r_object$data[r_object$data$Outliers == "Outlier", ][,2][i]*r_object$coef[1],linetype="solid",colour="#56B4E9")
B<- B + geom_text(x=r_object$data[r_object$data$Outliers == "Outlier", ][,2][i],y=(r_object$data[r_object$data$Outliers == "Outlier", ][,3][i]*0.9),label=round(r_object$data[r_object$data$Outliers == "Outlier", ][,4][i],digits=2),size=2.5)
}
}
}
#If axes scales should be fixed
if(scale_match==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Redefine scale and IVW circle radii
maximal<-atan(max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$Wj)))
R.All<-max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/sin(maximal)
R.IVW<-R.All+(R.All/12)
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
#Plot circle for IVW estimate
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate plot showing only outliers using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Outlier","IVW"),values=c("#56B4E9","#E69F00","white"))
#Draw lines indicating individual Q contributions and give text displaying each value
for(i in 1:length(r_object$data[r_object$data$Outliers == "Outlier", ][,3])){
B<- B + geom_segment(x = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], xend = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], y = r_object$data[r_object$data$Outliers == "Outlier", ][,3][i], yend =r_object$data[r_object$data$Outliers == "Outlier", ][,2][i]*r_object$coef[1],linetype="solid",colour="#56B4E9")
B<- B + geom_text(x=r_object$data[r_object$data$Outliers == "Outlier", ][,2][i],y=(r_object$data[r_object$data$Outliers == "Outlier", ][,3][i]*0.9),label=round(r_object$data[r_object$data$Outliers == "Outlier", ][,4][i],digits=2),size=2.5)
}
}
}
}
}
#If only outliers are to be shown
if(show_outliers==FALSE){
#If the full scale is to be shown
if(radial_scale==TRUE){
#If axes scales should be fixed
if(scale_match==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+
labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate a plot showing all variants, and IVW estimate using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Variant","Outlier","IVW"),values=c("#56B4E9","#E69F00","#000000"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw lines showing the ratio estimate for each individual variant
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
}
}
if(scale_match==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate a plot showing all variants, and IVW estimate using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Variant","Outlier","IVW"),values=c("#56B4E9","#E69F00","#000000"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw lines showing the ratio estimate for each individual variant
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
}
}
}#radial scale
#If the full scale should not be shown
if(radial_scale==FALSE){
#If axes scales should be fixed
if(scale_match==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate a plot showing all variants, and IVW estimate using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Variant","Outlier","IVW"),values=c("#56B4E9","#E69F00","#000000"))
}
}
#If axes scales should be fixed
if(scale_match==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate a plot showing all variants, and IVW estimate using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Variant","Outlier","IVW"),values=c("#56B4E9","#E69F00","#000000"))
}
}
}
}
return(B)
}
if(class(r_object)=="egger"){
maximal<-atan(max(abs(r_object$data[,3]))/max(r_object$data[,2]))
R.All<-max(abs(r_object$data[,3]- r_object$coef[1,1]))/sin(maximal)
R.Egger<-R.All+(R.All/12)
#Define scaling parameter
Label.Scaling_Egg<-R.Egger/24
Scalemin<-min(r_object$data[,3]/r_object$data[,2],r_object$confint[1])
Scalemax<-max(r_object$data[,3]/r_object$data[,2],r_object$confint[2])
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
#Plot circle for Egger estimate
circledat_EGGEREST <- circle.radial(c(0,r_object$coef[1,1]),R.Egger,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxEgger<-circledat_EGGEREST$x
cyEgger<-circledat_EGGEREST$y
#Define minimum and maximum range of values for y axis
Y_MINEGGER<-min( c(min(r_object$data[,3]),(sin(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg))+r_object$coef[1,1],r_object$coef[1,1]-Label.Scaling_Egg))
Y_MAXEGGER<-max( c(max(r_object$data[,3]),(sin(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg))+r_object$coef[1,1],r_object$coef[1,1]+Label.Scaling_Egg))
#If all variants are to be shown
if(show_outliers==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Generates a plot showing all variants not using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="MR-Egger Radial") + geom_point(aes(colour="variant"))+geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg), y=sin(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg) +
r_object$coef[1,1],label=round(r_object$coef[2,1],digits=3),size=4)+geom_text(x=cos(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[1],digits=3),size=3)+geom_text(x=cos(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[2],digits=3),size=3)+theme_bw() +
theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[2,1]))*R.Egger, y = r_object$coef[1,1], yend = (sin(atan(r_object$coef[2,1]))*R.Egger)+r_object$coef[1,1],colour="MR-Egger"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINEGGER,Y_MAXEGGER))+scale_color_manual(breaks=c("variant","MR-Egger"),values=c("MR-Egger"="#D55E00","variant"="#000000"))+
theme(legend.title=element_blank())
#Indicates that no outliers are present
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
maximal<-atan(max(abs(r_object$data[r_object$data$Outliers == "Outlier", ][,3]))/max(abs(r_object$data[r_object$data$Outliers == "Outlier", ][,2])))
R.All<-max(abs(r_object$data[r_object$data$Outliers == "Outlier", ][,3]- r_object$coef[1,1]))/sin(maximal)
R.Egger<-R.All+(R.All/12)
#Define scaling parameter
Label.Scaling_Egg<-R.Egger/24
#Plot circle for Egger estimate
circledat_EGGEREST <- circle.radial(c(0,r_object$coef[1,1]),R.Egger,length(r_object$data[r_object$data$Outliers == "Outlier", ][,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxEgger<-circledat_EGGEREST$x
cyEgger<-circledat_EGGEREST$y
#Generate a plot showing only outlying variants and MR-Egger estimate without full scale
B<-ggplot(r_object$data[r_object$data$Outliers == "Outlier", ],aes(x=Wj,y=BetaWj)
)+labs(title="MR-Egger Radial") + geom_point(aes(colour=Outliers))+geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg), y=sin(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg)+
r_object$coef[1,1],label=round(r_object$coef[2,1],digits=3),size=4)+geom_text(x=cos(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[1],digits=3),size=3)+geom_text(x=cos(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[2],digits=3),size=3)+theme_bw() +
theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[2,1]))*R.Egger, y = r_object$coef[1,1], yend = (sin(atan(r_object$coef[2,1]))*R.Egger)+r_object$coef[1,1],colour="MR-Egger"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+
scale_y_continuous(limits = c(Y_MINEGGER,Y_MAXEGGER))+scale_colour_manual(breaks=c("Variant","Outlier","MR-Egger"),values=c("#D55E00","#E69F00","#000000"))+
theme(legend.title=element_blank())
#Draw lines indicating individual Q contributions and give text displaying each value
for(i in 1:length(r_object$data[r_object$data$Outliers == "Outlier", ][,3])){
B<- B + geom_segment(x = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], xend = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], y = r_object$data[r_object$data$Outliers == "Outlier", ][,3][i], yend =r_object$data[r_object$data$Outliers == "Outlier", ][,2][i]*r_object$coef[2,1]+r_object$coef[1,1],linetype="solid",colour="#D55E00")
B<- B + geom_text(x=r_object$data[r_object$data$Outliers == "Outlier", ][,2][i],y=(r_object$data[r_object$data$Outliers == "Outlier", ][,3][i]*0.9),label=round(r_object$data[r_object$data$Outliers == "Outlier", ][,4][i],digits=2),size=2.5)
}
}
}
#If all variants are to be shown
if(show_outliers==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Generates a plot showing all variants not using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="MR-Egger Radial") + geom_point(aes(colour="variant"))+geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg), y=sin(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg) +
r_object$coef[1,1],label=round(r_object$coef[2,1],digits=3),size=4)+geom_text(x=cos(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[1],digits=3),size=3)+geom_text(x=cos(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[2],digits=3),size=3)+theme_bw() +
theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[2,1]))*R.Egger, y = r_object$coef[1,1], yend = (sin(atan(r_object$coef[2,1]))*R.Egger)+r_object$coef[1,1],colour="MR-Egger"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINEGGER,Y_MAXEGGER))+scale_color_manual(breaks=c("variant","MR-Egger"),values=c("MR-Egger"="#D55E00","variant"="#000000"))+
theme(legend.title=element_blank())
#Indicates that no outliers are present
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Generate a plot showing all variants not using full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="MR-Egger Radial") + geom_point(aes(colour=Outliers))+geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg), y=sin(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg)+
r_object$coef[1,1],label=round(r_object$coef[2,1],digits=3),size=4)+geom_text(x=cos(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[1],digits=3),size=3)+geom_text(x=cos(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[2],digits=3),size=3)+theme_bw() +
theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[2,1]))*R.Egger, y = r_object$coef[1,1], yend = (sin(atan(r_object$coef[2,1]))*R.Egger)+r_object$coef[1,1],colour="MR-Egger"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINEGGER,Y_MAXEGGER))+scale_colour_manual(breaks=c("Variant","Outlier","MR-Egger"),values=c("#D55E00","#E69F00","#000000"))+
theme(legend.title=element_blank())
}
}
}
}
if(length(r_object)==19){
names(r_object)<-c("IVW.coef","IVW.qstatistic","IVW.df","IVW.outliers","data","IVW.confint","it.coef","Fex.coef",
"Rex.coef","It.confint","Fex.confint","Rex.confint","meanF","egger.coef","egger.qstatistic","egger.df","egger.outliers","egger.data","egger.confint")
r_object$IVW.coef<-c(r_object$IVW.coef[2,])
r_object$IVW.coef<-as.numeric(r_object$IVW.coef)
#Define scale, IVW and MR-Egger circle radii
maximal<-atan(max(abs(r_object$data[,3]))/max(abs(r_object$data[,2])))
R.All<-max(abs(r_object$data[,3]- r_object$egger.coef[1,1]))/sin(maximal)+median(r_object$data[,2])
R.IVW<-R.All+(R.All/12)
R.Egger<-R.All+(R.All/4)
#Define general scaling parameter
Label.Scaling<-R.IVW/24
#Define scaling parameter for MR-Egger
Label.Scaling_Egg<-R.Egger/8
Scalemin<-min(r_object$data[,3]/r_object$data[,2],r_object$IVW.confint[1],r_object$egger.confint[1])
Scalemax<-max(r_object$data[,3]/r_object$data[,2],r_object$IVW.confint[2],r_object$egger.confint[2])
#Define minimum and maximum values of y axis for scaling
Y_MIN<-sin(atan(Scalemin))*(R.IVW+Label.Scaling_Egg)
Y_MAX<-sin(atan(Scalemax))*(R.IVW+Label.Scaling_Egg)
Y_Range<-Scalemax-Scalemin
#Function for rounding to nearest 0.05 increment
mround <- function(x){
0.5*round(x/0.5)
}
#Define circle plotting points for scale, IVW and MR-Egger estimates
circledat_EGGEREST <- circle.radial(c(0, r_object$egger.coef[1,1]),R.Egger,length(r_object$data[,3]),atan(r_object$egger.confint[1]),atan(r_object$egger.confint[2]))
cxEgger<-circledat_EGGEREST$x
cyEgger<-circledat_EGGEREST$y
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$IVW.confint[1]),atan(r_object$IVW.confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
which(grepl("Outlier", r_object$egger.data[,6]))
r_object$data$out_types<-rep(0,length(r_object$data[,6]))
for(i in 1:length(r_object$data[,3])){
if(r_object$data[,6][i]=="Variant" & r_object$egger.data[,6][i]=="Variant"){
r_object$data$out_types[i]<-"Variant"
}
if(r_object$data[,6][i]=="Variant" & r_object$egger.data[,6][i]=="Outlier"){
r_object$data$out_types[i]<-"MR-Egger Outlier"
}
if(r_object$data[,6][i]=="Outlier" & r_object$egger.data[,6][i]=="Variant"){
r_object$data$out_types[i]<-"IVW Outlier"
}
if(r_object$data[,6][i]=="Outlier" & r_object$egger.data[,6][i]=="Outlier"){
r_object$data$out_types[i]<-"IVW and MR-Egger Outlier"
}
}
r_object$data$out_types<-factor(r_object$data$out_types)
#If only outliers are to be shown
if(show_outliers==TRUE){
#If the full scale is to be shown
if(radial_scale==TRUE){
#If axes scales should be fixed
if(scale_match==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])==length(r_object$data[,3])){
#Generate a plot showing both IVW and MR-Egger estimates, using the full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour="Variant"))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+coord_fixed()+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+
r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="#000000"))+ theme(legend.title=element_blank())
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])<length(r_object$data[,3])){
temp.dat<-r_object$data[unique(c(which(grepl("Outlier", r_object$egger.data[,6])),
which(grepl("Outlier", r_object$data[,6])))), ]
#Redefine IVW, MR-Egger and scale radii
maximal<-atan(max(abs(temp.dat[,3]))/max(abs(temp.dat[,2])))
R.All<-max(abs(r_object$data[,3]- r_object$egger.coef[1,1]))/sin(maximal)+median(r_object$data[,2])
R.IVW<-R.All+(R.All/12)
R.Egger<-R.All+(R.All/4)
#Redefine general label scaling parameter
Label.Scaling<-R.IVW/24
#Redefine MR-Egger label scaling parameter
Label.Scaling_Egg<-R.Egger/8
#Redefine values for plotting IVW, MR-Egger and scale circles
circledat_EGGEREST <- circle.radial(c(0, r_object$egger.coef[1,1]),R.Egger,length(temp.dat[,3]),atan(r_object$egger.confint[1]),atan(r_object$egger.confint[2]))
cxEgger<-circledat_EGGEREST$x
cyEgger<-circledat_EGGEREST$y
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(temp.dat[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(temp.dat[,3]),atan(r_object$IVW.confint[1]),atan(r_object$IVW.confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MIN<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAX<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generates a plot showing the MR-Egger and IVW estimates, showing only outliers and using the full scale
B<-ggplot(temp.dat,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=out_types))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+coord_fixed()+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("IVW and MR-Egger Outlier","MR-Egger Outlier","IVW Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="white","IVW and MR-Egger Outlier"="#CC79A7","MR-Egger Outlier"="#E69F00","IVW Outlier"="#009E73"))+ theme(legend.title=element_blank())
if(max(abs(temp.dat[,3]/temp.dat[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(temp.dat[,3]/temp.dat[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw individual ratio estimate lines for each outlier and Q distance indicator lines
Theta<-rep(0,length(temp.dat[,3]))
for(i in 1:length(temp.dat[,3])){
Theta<-atan(temp.dat[,3]/temp.dat[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
}
}
#If axes scales should be fixed
if(scale_match==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])==length(r_object$data[,3])){
#Generate a plot showing both IVW and MR-Egger estimates, using the full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour="Variant"))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+
r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="#000000"))+ theme(legend.title=element_blank())
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])<length(r_object$data[,3])){
temp.dat<-r_object$data[unique(c(which(grepl("Outlier", r_object$egger.data[,6])),
which(grepl("Outlier", r_object$data[,6])))), ]
#Redefine IVW, MR-Egger and scale radii
maximal<-atan(max(abs(temp.dat[,3]))/max(abs(temp.dat[,2])))
R.All<-max(abs(r_object$data[,3]- r_object$egger.coef[1,1]))/sin(maximal)+median(r_object$data[,2])
R.IVW<-R.All+(R.All/12)
R.Egger<-R.All+(R.All/4)
#Redefine general label scaling parameter
Label.Scaling<-R.IVW/24
#Redefine MR-Egger label scaling parameter
Label.Scaling_Egg<-R.Egger/8
#Redefine values for plotting IVW, MR-Egger and scale circles
circledat_EGGEREST <- circle.radial(c(0, r_object$egger.coef[1,1]),R.Egger,length(temp.dat[,3]),atan(r_object$egger.confint[1]),atan(r_object$egger.confint[2]))
cxEgger<-circledat_EGGEREST$x
cyEgger<-circledat_EGGEREST$y
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(temp.dat[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(temp.dat[,3]),atan(r_object$IVW.confint[1]),atan(r_object$IVW.confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MIN<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAX<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generates a plot showing the MR-Egger and IVW estimates, showing only outliers and using the full scale
B<-ggplot(temp.dat,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=out_types))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("IVW and MR-Egger Outlier","MR-Egger Outlier","IVW Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="white","IVW and MR-Egger Outlier"="#CC79A7","MR-Egger Outlier"="#E69F00","IVW Outlier"="#009E73"))+ theme(legend.title=element_blank())
if(max(abs(temp.dat[,3]/temp.dat[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(temp.dat[,3]/temp.dat[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw individual ratio estimate lines for each outlier and Q distance indicator lines
Theta<-rep(0,length(temp.dat[,3]))
for(i in 1:length(temp.dat[,3])){
Theta<-atan(temp.dat[,3]/temp.dat[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
}
}
}
#If the full scale is to be shown
if(radial_scale==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])==length(r_object$data[,3])){
MINCILIM<-min(sin(atan(r_object$IVW.confint[1]))*R.IVW + Label.Scaling,sin(atan(r_object$egger.confint[1]-1))*(R.Egger +Label.Scaling_Egg-r_object$egger.coef[1,1]),r_object$egger.coef[1,1])
MAXCILIM<-max(sin(atan(r_object$IVW.confint[2]))*R.IVW + Label.Scaling,sin(atan(r_object$egger.confint[2]+1))*(R.Egger +Label.Scaling_Egg-r_object$egger.coef[1,1]),r_object$egger.coef[1,1])
if(min(r_object$data[,3]) < MINCILIM){
Y_MIN<-min(r_object$data[,3])
}
if(min(r_object$data[,3]) > MINCILIM){
Y_MIN<-MINCILIM
}
if(max(r_object$data[,3]) >MAXCILIM){
Y_MAX<-max(r_object$data[,3])
}
if(max(r_object$data[,3]) <MAXCILIM){
Y_MAX<-MAXCILIM
}
Y_Range<-Y_MAX-Y_MIN
#Generate a plot showing the MR-Egger and IVW estimates, showing all variants and not using a full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=Outliers)) +geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+
r_object$egger.coef[1,1],colour="MR-Egger"))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+scale_color_manual(breaks=c("Variant","Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="#000000","Outlier"="#E69F00"))+
theme(legend.title=element_blank())
#Indicate that no outliers are present
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])<length(r_object$data[,3])){
temp.dat<-r_object$data[unique(c(which(grepl("Outlier", r_object$egger.data[,6])),
which(grepl("Outlier", r_object$data[,6])))), ]
#Redefine IVW, MR-Egger and scale radii
maximal<-atan(max(abs(temp.dat[,3]))/max(abs(temp.dat[,2])))
R.All<-max(abs(r_object$data[,3]- r_object$egger.coef[1,1]))/sin(maximal)+median(r_object$data[,2])
R.IVW<-R.All+(R.All/12)
R.Egger<-R.All+(R.All/4)
#Redefine general label scaling parameter
Label.Scaling<-R.IVW/24
#Redefine MR-Egger label scaling parameter
Label.Scaling_Egg<-R.Egger/8
#Redefine values for plotting IVW, MR-Egger and scale circles
circledat_EGGEREST <- circle.radial(c(0, r_object$egger.coef[1,1]),R.Egger,length(temp.dat[,3]),atan(r_object$egger.confint[1]),atan(r_object$egger.confint[2]))
cxEgger<-circledat_EGGEREST$x
cyEgger<-circledat_EGGEREST$y
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(temp.dat[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(temp.dat[,3]),atan(r_object$IVW.confint[1]),atan(r_object$IVW.confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
MINCILIM<-min(sin(atan(r_object$IVW.confint[1]))*R.IVW + Label.Scaling,sin(atan(r_object$egger.confint[1]-1))*(R.Egger +Label.Scaling_Egg-r_object$egger.coef[1,1]),r_object$egger.coef[1,1])
MAXCILIM<-max(sin(atan(r_object$IVW.confint[2]))*R.IVW + Label.Scaling,sin(atan(r_object$egger.confint[2]+1))*(R.Egger +Label.Scaling_Egg-r_object$egger.coef[1,1]),r_object$egger.coef[1,1])
if(min(temp.dat[,3]) < MINCILIM){
Y_MIN<-min(temp.dat[,3])
}
if(min(temp.dat[,3]) > MINCILIM){
Y_MIN<-MINCILIM
}
if(max(temp.dat[,3]) >MAXCILIM){
Y_MAX<-max(temp.dat[,3])
}
if(max(temp.dat[,3]) <MAXCILIM){
Y_MAX<-MAXCILIM
}
Y_Range<-Y_MAX-Y_MIN
#Generate a plot showing both IVW and MR-Egger estimates, only showing outlying variants and not using the full scale
B<-ggplot(temp.dat,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=out_types)) +geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+theme_bw() +
theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+r_object$egger.coef[1,1],colour="MR-Egger"))+
scale_y_continuous(limits = c(Y_MIN,Y_MAX))+scale_color_manual(breaks=c("IVW and MR-Egger Outlier","MR-Egger Outlier","IVW Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="white","IVW and MR-Egger Outlier"="#CC79A7","MR-Egger Outlier"="#E69F00","IVW Outlier"="#009E73"))+ theme(legend.title=element_blank())
#Draw lines showing Q statistic contributions for each variant using respective colours
for(i in 1:length(temp.dat[,3])){
if(abs((temp.dat[,3][i]-temp.dat[,2][i]*r_object$IVW.coef[1]))>abs((temp.dat[,3][i]-(temp.dat[,2][i]*r_object$egger.coef[2,1]+r_object$egger.coef[1,1])))){
B<- B + geom_segment(x = temp.dat[,2][i], xend = temp.dat[,2][i], y = temp.dat[,3][i], yend =temp.dat[,2][i]*r_object$IVW.coef[1],linetype="solid",colour="#56B4E9")
B<- B + geom_segment(x = temp.dat[,2][i], xend = temp.dat[,2][i], y = temp.dat[,3][i], yend =temp.dat[,2][i]*r_object$egger.coef[2,1]+r_object$egger.coef[1,1],linetype="solid",colour="#D55E00")
}
if(abs((temp.dat[,3][i]-temp.dat[,2][i]*r_object$IVW.coef[1]))<abs((temp.dat[,3][i]-(temp.dat[,2][i]*r_object$egger.coef[2,1]+r_object$egger.coef[1,1])))){
B<- B + geom_segment(x = temp.dat[,2][i], xend = temp.dat[,2][i], y = temp.dat[,3][i], yend =temp.dat[,2][i]*r_object$egger.coef[2,1]+r_object$egger.coef[1,1],linetype="solid",colour="#D55E00")
B<- B + geom_segment(x = temp.dat[,2][i], xend = temp.dat[,2][i], y = temp.dat[,3][i], yend =temp.dat[,2][i]*r_object$IVW.coef[1],linetype="solid",colour="#56B4E9")
}
}
}
}
}
#If only outliers are to be shown
if(show_outliers==FALSE){
#If the full scale is to be shown
if(radial_scale==TRUE){
#If axes scales should be fixed
if(scale_match==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])==length(r_object$data[,3])){
#Generate a plot showing both IVW and MR-Egger estimates, using the full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour="Variant"))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+coord_fixed()+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+
r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="#000000"))+ theme(legend.title=element_blank())
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])<length(r_object$data[,3])){
#Generates a plot showing the MR-Egger and IVW estimates, showing only outliers and using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=out_types))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+coord_fixed()+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW and MR-Egger Outlier","MR-Egger Outlier","IVW Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="black","IVW and MR-Egger Outlier"="#CC79A7","MR-Egger Outlier"="#E69F00","IVW Outlier"="#009E73"))+ theme(legend.title=element_blank())
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw individual ratio estimate lines for each outlier and Q distance indicator lines
Theta<-rep(0,length(r_object$data[,3]))
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
}
}
#If axes scales should be fixed
if(scale_match==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])==length(r_object$data[,3])){
#Generate a plot showing both IVW and MR-Egger estimates, using the full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour="Variant"))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+
r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="#000000"))+ theme(legend.title=element_blank())
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])<length(r_object$data[,3])){
#Generates a plot showing the MR-Egger and IVW estimates, showing only outliers and using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=out_types))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW and MR-Egger Outlier","MR-Egger Outlier","IVW Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="black","IVW and MR-Egger Outlier"="#CC79A7","MR-Egger Outlier"="#E69F00","IVW Outlier"="#009E73"))+ theme(legend.title=element_blank())
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw individual ratio estimate lines for each outlier and Q distance indicator lines
Theta<-rep(0,length(r_object$data[,3]))
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
}
}
}
#If the full scale is to be shown
if(radial_scale==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])==length(r_object$data[,3])){
MINCILIM<-min(sin(atan(r_object$IVW.confint[1]))*R.IVW + Label.Scaling,sin(atan(r_object$egger.confint[1]-1))*(R.Egger +Label.Scaling_Egg-r_object$egger.coef[1,1]),r_object$egger.coef[1,1])
MAXCILIM<-max(sin(atan(r_object$IVW.confint[2]))*R.IVW + Label.Scaling,sin(atan(r_object$egger.confint[2]+1))*(R.Egger +Label.Scaling_Egg-r_object$egger.coef[1,1]),r_object$egger.coef[1,1])
if(min(r_object$data[,3]) < MINCILIM){
Y_MIN<-min(r_object$data[,3])
}
if(min(r_object$data[,3]) > MINCILIM){
Y_MIN<-MINCILIM
}
if(max(r_object$data[,3]) >MAXCILIM){
Y_MAX<-max(r_object$data[,3])
}
if(max(r_object$data[,3]) <MAXCILIM){
Y_MAX<-MAXCILIM
}
Y_Range<-Y_MAX-Y_MIN
#Generate a plot showing the MR-Egger and IVW estimates, showing all variants and not using a full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=Outliers)) +geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+
r_object$egger.coef[1,1],colour="MR-Egger"))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+scale_color_manual(breaks=c("Variant","Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="#000000","Outlier"="#E69F00"))+
theme(legend.title=element_blank())
#Indicate that no outliers are present
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])<length(r_object$data[,3])){
#Generates a plot showing the MR-Egger and IVW estimates, showing only outliers and using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=out_types))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW and MR-Egger Outlier","MR-Egger Outlier","IVW Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="black","IVW and MR-Egger Outlier"="#CC79A7","MR-Egger Outlier"="#E69F00","IVW Outlier"="#009E73"))+ theme(legend.title=element_blank())
}
}
}
}
return(B)
}
WSpiller/MRPracticals documentation built on April 25, 2020, 10:52 a.m.
R Package Documentation
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Defines functions plot_radial
Documented in plot_radial
#' plot_radial
#'
#' A function for producing radial IVW and MR-Egger plots either individually or simultaneously. The function allows for a variety of aesthetic and scaling options, utilising the output from the \code{IVW_radial} and \code{egger_radial} functions.
#'
#' @param r_object An object of class \code{"IVW"} or \code{"egger"}. For visualising both estimates simultaneously, both objects should be included as a vector c(\code{A},\code{B}), where \code{A} and \code{B} denote the \code{"IVW"} and \code{"egger"} objects respectively.
#' @param radial_scale Indicates whether to produce a plot including a full radial scale (\code{TRUE}), or a scatterplot showing only the effect estimates (\code{FALSE}).
#' @param show_outliers Indicates whether display only the set of variants identified as outliers (\code{TRUE}) or the complete set of variants (\code{FALSE}). Note that when (\code{show_outliers=TRUE}), non-outlying variants further from the origin than the furthest outlier will cause an error message that one or more points have been omitted. These are non-outlying variants beyond the scale. If no outliers are present, a plot will be produced using the full set of variants, with an accompanying message indicating the absence of outliers.
#' @param scale_match Indicates whether x and y axes should have the same range(\code{TRUE}), or different ranges (\code{FALSE}) This improves the interpretation of the radial scale, and is set to \code{FALSE} when the radial scale is omitted from the plot.
#' @return A ggplot object containing a radial plot of either the IVW, MR-Egger, or both estimates simultaneously.
#'@author Wes Spiller; Jack Bowden.
#'@references Bowden, J., et al., Improving the visualization, interpretation and analysis of two-sample summary data Mendelian randomization via the Radial plot and Radial regression. International Journal of Epidemiology, 2018. 47(4): p. 1264-1278.
#'@export
#'@examples
#'
#'plot_radial(r_object,TRUE,TRUE,TRUE)
#'
#'plot_radial(c(r_object,r_object),TRUE,TRUE,FALSE)
plot_radial<-function(r_object,radial_scale,show_outliers,scale_match){
if(missing(radial_scale)) {
radial_scale<-T
}
if(missing(show_outliers)) {
show_outliers<-F
}
if(missing(scale_match)) {
scale_match<-T
}
#Load ggplot2 library
library(ggplot2)
#Function for producing scale and confidence interval circle indicators
circle.radial <- function(center = c(0,0), radius, num.points, START,END){
R = radius
tt <- seq(START,END,length.out = num.points)
#Generates x-axis values for circle
xx <- center[1] + R * cos(tt)
#Generates y-axis values for circle
yy <- center[2] + R * sin(tt)
return(data.frame(x = xx, y = yy))
}
if(length(r_object)>=6 && length(r_object)<=13){
if(class(r_object)=="IVW"){
r_object$coef<-c(r_object$coef[2,])
r_object$coef<-as.numeric(r_object$coef)
#Define radius for scale and IVW circles
maximal<-atan(max(abs(r_object$data[,3]))/max(r_object$data[,2]))
R.All<-max(abs(r_object$data[,3]))/sin(maximal)
R.IVW<-R.All+(R.All/12)
#Define scaling parameter
Label.Scaling<-R.IVW/24
Scalemin<-min(r_object$data[,3]/r_object$data[,2],r_object$confint[1])
Scalemax<-max(r_object$data[,3]/r_object$data[,2],r_object$confint[2])
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
#Plot circle for IVW estimate
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Function for rounding to nearest 0.05 increment
mround <- function(x){
0.5*round(x/0.5)
}
#If only outliers are to be shown
if(show_outliers==TRUE){
#If the full scale is to be shown
if(radial_scale==TRUE){
#If axes scales should be fixed
if(scale_match==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Redefine scale and IVW circle radii
maximal<-atan(max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$Wj)))
R.All<-max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/sin(maximal)
R.IVW<-R.All+(R.All/12)
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
#Plot circle for IVW estimate
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate plot showing only outliers using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Outlier","IVW"),values=c("#56B4E9","#E69F00","white"))
#Function for rounding to nearest 0.05 increment
mround <- function(x){
0.5*round(x/0.5)
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw individual ratio estimate lines for each outlier and Q distance indicator lines
Theta<-rep(0,length(r_object$data[r_object$data$Outliers == "Outlier", ]$Outliers))
for(i in 1:length(r_object$data[r_object$data$Outliers == "Outlier", ][,3])){
Theta<-atan(r_object$data[r_object$data$Outliers == "Outlier", ][,3]/r_object$data[r_object$data$Outliers == "Outlier", ][,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
B<- B + geom_segment(x = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], xend = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i],
y = r_object$data[r_object$data$Outliers == "Outlier", ][,3][i], yend =r_object$data[r_object$data$Outliers == "Outlier", ][,2][i]*
r_object$coef[1],linetype="solid",colour="#56B4E9")
}
}
}
#If axes scales should be fixed
if(scale_match==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Redefine scale and IVW circle radii
maximal<-atan(max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$Wj)))
R.All<-max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/sin(maximal)
R.IVW<-R.All+(R.All/12)
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
#Plot circle for IVW estimate
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate plot showing only outliers using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Outlier","IVW"),values=c("#56B4E9","#E69F00","white"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw individual ratio estimate lines for each outlier and Q distance indicator lines
Theta<-rep(0,length(r_object$data[r_object$data$Outliers == "Outlier", ]$Outliers))
for(i in 1:length(r_object$data[r_object$data$Outliers == "Outlier", ][,3])){
Theta<-atan(r_object$data[r_object$data$Outliers == "Outlier", ][,3]/r_object$data[r_object$data$Outliers == "Outlier", ][,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
B<- B + geom_segment(x = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], xend = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i],
y = r_object$data[r_object$data$Outliers == "Outlier", ][,3][i], yend =r_object$data[r_object$data$Outliers == "Outlier", ][,2][i]*
r_object$coef[1],linetype="solid",colour="#56B4E9")
}
}
}
}
#If the full scale is to be shown
if(radial_scale==FALSE){
#If axes scales should be fixed
if(scale_match==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Redefine scale and IVW circle radii
maximal<-atan(max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$Wj)))
R.All<-max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/sin(maximal)
R.IVW<-R.All+(R.All/12)
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
#Plot circle for IVW estimate
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate plot showing only outliers using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Outlier","IVW"),values=c("#56B4E9","#E69F00","white"))
#Draw lines indicating individual Q contributions and give text displaying each value
for(i in 1:length(r_object$data[r_object$data$Outliers == "Outlier", ][,3])){
B<- B + geom_segment(x = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], xend = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], y = r_object$data[r_object$data$Outliers == "Outlier", ][,3][i], yend =r_object$data[r_object$data$Outliers == "Outlier", ][,2][i]*r_object$coef[1],linetype="solid",colour="#56B4E9")
B<- B + geom_text(x=r_object$data[r_object$data$Outliers == "Outlier", ][,2][i],y=(r_object$data[r_object$data$Outliers == "Outlier", ][,3][i]*0.9),label=round(r_object$data[r_object$data$Outliers == "Outlier", ][,4][i],digits=2),size=2.5)
}
}
}
#If axes scales should be fixed
if(scale_match==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Redefine scale and IVW circle radii
maximal<-atan(max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$Wj)))
R.All<-max(abs(r_object$data[r_object$data$Outliers == "Outlier", ]$BetaWj))/sin(maximal)
R.IVW<-R.All+(R.All/12)
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
#Plot circle for IVW estimate
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate plot showing only outliers using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Outlier","IVW"),values=c("#56B4E9","#E69F00","white"))
#Draw lines indicating individual Q contributions and give text displaying each value
for(i in 1:length(r_object$data[r_object$data$Outliers == "Outlier", ][,3])){
B<- B + geom_segment(x = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], xend = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], y = r_object$data[r_object$data$Outliers == "Outlier", ][,3][i], yend =r_object$data[r_object$data$Outliers == "Outlier", ][,2][i]*r_object$coef[1],linetype="solid",colour="#56B4E9")
B<- B + geom_text(x=r_object$data[r_object$data$Outliers == "Outlier", ][,2][i],y=(r_object$data[r_object$data$Outliers == "Outlier", ][,3][i]*0.9),label=round(r_object$data[r_object$data$Outliers == "Outlier", ][,4][i],digits=2),size=2.5)
}
}
}
}
}
#If only outliers are to be shown
if(show_outliers==FALSE){
#If the full scale is to be shown
if(radial_scale==TRUE){
#If axes scales should be fixed
if(scale_match==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+
labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate a plot showing all variants, and IVW estimate using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Variant","Outlier","IVW"),values=c("#56B4E9","#E69F00","#000000"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw lines showing the ratio estimate for each individual variant
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
}
}
if(scale_match==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate a plot showing all variants, and IVW estimate using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Variant","Outlier","IVW"),values=c("#56B4E9","#E69F00","#000000"))
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw lines showing the ratio estimate for each individual variant
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
}
}
}#radial scale
#If the full scale should not be shown
if(radial_scale==FALSE){
#If axes scales should be fixed
if(scale_match==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate a plot showing all variants, and IVW estimate using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
coord_fixed()+theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Variant","Outlier","IVW"),values=c("#56B4E9","#E69F00","#000000"))
}
}
#If axes scales should be fixed
if(scale_match==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Produce plot showing full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj))+labs(title="IVW Radial")+ geom_point(aes(colour="Variant"))+
geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5),
label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling)-c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1]),
label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)+c(quantile(r_object$data$Wj,seq(0,0.1,0.1))[1])),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
scale_color_manual(name="Estimate",breaks=c("Variant","IVW"),values=c("IVW"="#56B4E9","Variant"="#000000"))
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MINIVW<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAXIVW<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generate a plot showing all variants, and IVW estimate using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="IVW Radial") + geom_point(aes(colour = Outliers))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$confint[2],digits=3),size=3)+
theme_bw()+theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,R.IVW+(Label.Scaling*5)),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINIVW,Y_MAXIVW))+
theme(legend.title=element_blank())+scale_colour_manual(breaks=c("Variant","Outlier","IVW"),values=c("#56B4E9","#E69F00","#000000"))
}
}
}
}
return(B)
}
if(class(r_object)=="egger"){
maximal<-atan(max(abs(r_object$data[,3]))/max(r_object$data[,2]))
R.All<-max(abs(r_object$data[,3]- r_object$coef[1,1]))/sin(maximal)
R.Egger<-R.All+(R.All/12)
#Define scaling parameter
Label.Scaling_Egg<-R.Egger/24
Scalemin<-min(r_object$data[,3]/r_object$data[,2],r_object$confint[1])
Scalemax<-max(r_object$data[,3]/r_object$data[,2],r_object$confint[2])
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
#Plot circle for Egger estimate
circledat_EGGEREST <- circle.radial(c(0,r_object$coef[1,1]),R.Egger,length(r_object$data[,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxEgger<-circledat_EGGEREST$x
cyEgger<-circledat_EGGEREST$y
#Define minimum and maximum range of values for y axis
Y_MINEGGER<-min( c(min(r_object$data[,3]),(sin(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg))+r_object$coef[1,1],r_object$coef[1,1]-Label.Scaling_Egg))
Y_MAXEGGER<-max( c(max(r_object$data[,3]),(sin(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg))+r_object$coef[1,1],r_object$coef[1,1]+Label.Scaling_Egg))
#If all variants are to be shown
if(show_outliers==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Generates a plot showing all variants not using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="MR-Egger Radial") + geom_point(aes(colour="variant"))+geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg), y=sin(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg) +
r_object$coef[1,1],label=round(r_object$coef[2,1],digits=3),size=4)+geom_text(x=cos(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[1],digits=3),size=3)+geom_text(x=cos(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[2],digits=3),size=3)+theme_bw() +
theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[2,1]))*R.Egger, y = r_object$coef[1,1], yend = (sin(atan(r_object$coef[2,1]))*R.Egger)+r_object$coef[1,1],colour="MR-Egger"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINEGGER,Y_MAXEGGER))+scale_color_manual(breaks=c("variant","MR-Egger"),values=c("MR-Egger"="#D55E00","variant"="#000000"))+
theme(legend.title=element_blank())
#Indicates that no outliers are present
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
maximal<-atan(max(abs(r_object$data[r_object$data$Outliers == "Outlier", ][,3]))/max(abs(r_object$data[r_object$data$Outliers == "Outlier", ][,2])))
R.All<-max(abs(r_object$data[r_object$data$Outliers == "Outlier", ][,3]- r_object$coef[1,1]))/sin(maximal)
R.Egger<-R.All+(R.All/12)
#Define scaling parameter
Label.Scaling_Egg<-R.Egger/24
#Plot circle for Egger estimate
circledat_EGGEREST <- circle.radial(c(0,r_object$coef[1,1]),R.Egger,length(r_object$data[r_object$data$Outliers == "Outlier", ][,3]),atan(r_object$confint[1]),atan(r_object$confint[2]))
cxEgger<-circledat_EGGEREST$x
cyEgger<-circledat_EGGEREST$y
#Generate a plot showing only outlying variants and MR-Egger estimate without full scale
B<-ggplot(r_object$data[r_object$data$Outliers == "Outlier", ],aes(x=Wj,y=BetaWj)
)+labs(title="MR-Egger Radial") + geom_point(aes(colour=Outliers))+geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg), y=sin(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg)+
r_object$coef[1,1],label=round(r_object$coef[2,1],digits=3),size=4)+geom_text(x=cos(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[1],digits=3),size=3)+geom_text(x=cos(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[2],digits=3),size=3)+theme_bw() +
theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[2,1]))*R.Egger, y = r_object$coef[1,1], yend = (sin(atan(r_object$coef[2,1]))*R.Egger)+r_object$coef[1,1],colour="MR-Egger"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+
scale_y_continuous(limits = c(Y_MINEGGER,Y_MAXEGGER))+scale_colour_manual(breaks=c("Variant","Outlier","MR-Egger"),values=c("#D55E00","#E69F00","#000000"))+
theme(legend.title=element_blank())
#Draw lines indicating individual Q contributions and give text displaying each value
for(i in 1:length(r_object$data[r_object$data$Outliers == "Outlier", ][,3])){
B<- B + geom_segment(x = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], xend = r_object$data[r_object$data$Outliers == "Outlier", ][,2][i], y = r_object$data[r_object$data$Outliers == "Outlier", ][,3][i], yend =r_object$data[r_object$data$Outliers == "Outlier", ][,2][i]*r_object$coef[2,1]+r_object$coef[1,1],linetype="solid",colour="#D55E00")
B<- B + geom_text(x=r_object$data[r_object$data$Outliers == "Outlier", ][,2][i],y=(r_object$data[r_object$data$Outliers == "Outlier", ][,3][i]*0.9),label=round(r_object$data[r_object$data$Outliers == "Outlier", ][,4][i],digits=2),size=2.5)
}
}
}
#If all variants are to be shown
if(show_outliers==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])==0){
#Generates a plot showing all variants not using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="MR-Egger Radial") + geom_point(aes(colour="variant"))+geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg), y=sin(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg) +
r_object$coef[1,1],label=round(r_object$coef[2,1],digits=3),size=4)+geom_text(x=cos(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[1],digits=3),size=3)+geom_text(x=cos(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[2],digits=3),size=3)+theme_bw() +
theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[2,1]))*R.Egger, y = r_object$coef[1,1], yend = (sin(atan(r_object$coef[2,1]))*R.Egger)+r_object$coef[1,1],colour="MR-Egger"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINEGGER,Y_MAXEGGER))+scale_color_manual(breaks=c("variant","MR-Egger"),values=c("MR-Egger"="#D55E00","variant"="#000000"))+
theme(legend.title=element_blank())
#Indicates that no outliers are present
print("No significant Outliers")
}
#If no outliers are present
if(nrow(r_object$data[r_object$data$Outliers == "Outlier", ])>0){
#Generate a plot showing all variants not using full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="MR-Egger Radial") + geom_point(aes(colour=Outliers))+geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg), y=sin(atan(r_object$coef[2,1]))*(R.Egger+Label.Scaling_Egg)+
r_object$coef[1,1],label=round(r_object$coef[2,1],digits=3),size=4)+geom_text(x=cos(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[1]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[1],digits=3),size=3)+geom_text(x=cos(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg),y=(sin(atan(r_object$confint[2]))*(R.Egger+Label.Scaling_Egg))+
r_object$coef[1,1],label=round(r_object$confint[2],digits=3),size=3)+theme_bw() +
theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$coef[2,1]))*R.Egger, y = r_object$coef[1,1], yend = (sin(atan(r_object$coef[2,1]))*R.Egger)+r_object$coef[1,1],colour="MR-Egger"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MINEGGER,Y_MAXEGGER))+scale_colour_manual(breaks=c("Variant","Outlier","MR-Egger"),values=c("#D55E00","#E69F00","#000000"))+
theme(legend.title=element_blank())
}
}
}
}
if(length(r_object)==19){
names(r_object)<-c("IVW.coef","IVW.qstatistic","IVW.df","IVW.outliers","data","IVW.confint","it.coef","Fex.coef",
"Rex.coef","It.confint","Fex.confint","Rex.confint","meanF","egger.coef","egger.qstatistic","egger.df","egger.outliers","egger.data","egger.confint")
r_object$IVW.coef<-c(r_object$IVW.coef[2,])
r_object$IVW.coef<-as.numeric(r_object$IVW.coef)
#Define scale, IVW and MR-Egger circle radii
maximal<-atan(max(abs(r_object$data[,3]))/max(abs(r_object$data[,2])))
R.All<-max(abs(r_object$data[,3]- r_object$egger.coef[1,1]))/sin(maximal)+median(r_object$data[,2])
R.IVW<-R.All+(R.All/12)
R.Egger<-R.All+(R.All/4)
#Define general scaling parameter
Label.Scaling<-R.IVW/24
#Define scaling parameter for MR-Egger
Label.Scaling_Egg<-R.Egger/8
Scalemin<-min(r_object$data[,3]/r_object$data[,2],r_object$IVW.confint[1],r_object$egger.confint[1])
Scalemax<-max(r_object$data[,3]/r_object$data[,2],r_object$IVW.confint[2],r_object$egger.confint[2])
#Define minimum and maximum values of y axis for scaling
Y_MIN<-sin(atan(Scalemin))*(R.IVW+Label.Scaling_Egg)
Y_MAX<-sin(atan(Scalemax))*(R.IVW+Label.Scaling_Egg)
Y_Range<-Scalemax-Scalemin
#Function for rounding to nearest 0.05 increment
mround <- function(x){
0.5*round(x/0.5)
}
#Define circle plotting points for scale, IVW and MR-Egger estimates
circledat_EGGEREST <- circle.radial(c(0, r_object$egger.coef[1,1]),R.Egger,length(r_object$data[,3]),atan(r_object$egger.confint[1]),atan(r_object$egger.confint[2]))
cxEgger<-circledat_EGGEREST$x
cyEgger<-circledat_EGGEREST$y
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(r_object$data[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(r_object$data[,3]),atan(r_object$IVW.confint[1]),atan(r_object$IVW.confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
which(grepl("Outlier", r_object$egger.data[,6]))
r_object$data$out_types<-rep(0,length(r_object$data[,6]))
for(i in 1:length(r_object$data[,3])){
if(r_object$data[,6][i]=="Variant" & r_object$egger.data[,6][i]=="Variant"){
r_object$data$out_types[i]<-"Variant"
}
if(r_object$data[,6][i]=="Variant" & r_object$egger.data[,6][i]=="Outlier"){
r_object$data$out_types[i]<-"MR-Egger Outlier"
}
if(r_object$data[,6][i]=="Outlier" & r_object$egger.data[,6][i]=="Variant"){
r_object$data$out_types[i]<-"IVW Outlier"
}
if(r_object$data[,6][i]=="Outlier" & r_object$egger.data[,6][i]=="Outlier"){
r_object$data$out_types[i]<-"IVW and MR-Egger Outlier"
}
}
r_object$data$out_types<-factor(r_object$data$out_types)
#If only outliers are to be shown
if(show_outliers==TRUE){
#If the full scale is to be shown
if(radial_scale==TRUE){
#If axes scales should be fixed
if(scale_match==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])==length(r_object$data[,3])){
#Generate a plot showing both IVW and MR-Egger estimates, using the full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour="Variant"))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+coord_fixed()+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+
r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="#000000"))+ theme(legend.title=element_blank())
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])<length(r_object$data[,3])){
temp.dat<-r_object$data[unique(c(which(grepl("Outlier", r_object$egger.data[,6])),
which(grepl("Outlier", r_object$data[,6])))), ]
#Redefine IVW, MR-Egger and scale radii
maximal<-atan(max(abs(temp.dat[,3]))/max(abs(temp.dat[,2])))
R.All<-max(abs(r_object$data[,3]- r_object$egger.coef[1,1]))/sin(maximal)+median(r_object$data[,2])
R.IVW<-R.All+(R.All/12)
R.Egger<-R.All+(R.All/4)
#Redefine general label scaling parameter
Label.Scaling<-R.IVW/24
#Redefine MR-Egger label scaling parameter
Label.Scaling_Egg<-R.Egger/8
#Redefine values for plotting IVW, MR-Egger and scale circles
circledat_EGGEREST <- circle.radial(c(0, r_object$egger.coef[1,1]),R.Egger,length(temp.dat[,3]),atan(r_object$egger.confint[1]),atan(r_object$egger.confint[2]))
cxEgger<-circledat_EGGEREST$x
cyEgger<-circledat_EGGEREST$y
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(temp.dat[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(temp.dat[,3]),atan(r_object$IVW.confint[1]),atan(r_object$IVW.confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MIN<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAX<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generates a plot showing the MR-Egger and IVW estimates, showing only outliers and using the full scale
B<-ggplot(temp.dat,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=out_types))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+coord_fixed()+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("IVW and MR-Egger Outlier","MR-Egger Outlier","IVW Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="white","IVW and MR-Egger Outlier"="#CC79A7","MR-Egger Outlier"="#E69F00","IVW Outlier"="#009E73"))+ theme(legend.title=element_blank())
if(max(abs(temp.dat[,3]/temp.dat[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(temp.dat[,3]/temp.dat[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw individual ratio estimate lines for each outlier and Q distance indicator lines
Theta<-rep(0,length(temp.dat[,3]))
for(i in 1:length(temp.dat[,3])){
Theta<-atan(temp.dat[,3]/temp.dat[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
}
}
#If axes scales should be fixed
if(scale_match==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])==length(r_object$data[,3])){
#Generate a plot showing both IVW and MR-Egger estimates, using the full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour="Variant"))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+
r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="#000000"))+ theme(legend.title=element_blank())
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])<length(r_object$data[,3])){
temp.dat<-r_object$data[unique(c(which(grepl("Outlier", r_object$egger.data[,6])),
which(grepl("Outlier", r_object$data[,6])))), ]
#Redefine IVW, MR-Egger and scale radii
maximal<-atan(max(abs(temp.dat[,3]))/max(abs(temp.dat[,2])))
R.All<-max(abs(r_object$data[,3]- r_object$egger.coef[1,1]))/sin(maximal)+median(r_object$data[,2])
R.IVW<-R.All+(R.All/12)
R.Egger<-R.All+(R.All/4)
#Redefine general label scaling parameter
Label.Scaling<-R.IVW/24
#Redefine MR-Egger label scaling parameter
Label.Scaling_Egg<-R.Egger/8
#Redefine values for plotting IVW, MR-Egger and scale circles
circledat_EGGEREST <- circle.radial(c(0, r_object$egger.coef[1,1]),R.Egger,length(temp.dat[,3]),atan(r_object$egger.confint[1]),atan(r_object$egger.confint[2]))
cxEgger<-circledat_EGGEREST$x
cyEgger<-circledat_EGGEREST$y
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(temp.dat[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(temp.dat[,3]),atan(r_object$IVW.confint[1]),atan(r_object$IVW.confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
#Define minimum and maximum values of y axis for scaling
Y_MIN<-sin(atan(Scalemin))*(R.IVW+Label.Scaling)
Y_MAX<-sin(atan(Scalemax))*(R.IVW+Label.Scaling)
Y_Range<-Scalemax-Scalemin
#Generates a plot showing the MR-Egger and IVW estimates, showing only outliers and using the full scale
B<-ggplot(temp.dat,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=out_types))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("IVW and MR-Egger Outlier","MR-Egger Outlier","IVW Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="white","IVW and MR-Egger Outlier"="#CC79A7","MR-Egger Outlier"="#E69F00","IVW Outlier"="#009E73"))+ theme(legend.title=element_blank())
if(max(abs(temp.dat[,3]/temp.dat[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(temp.dat[,3]/temp.dat[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw individual ratio estimate lines for each outlier and Q distance indicator lines
Theta<-rep(0,length(temp.dat[,3]))
for(i in 1:length(temp.dat[,3])){
Theta<-atan(temp.dat[,3]/temp.dat[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
}
}
}
#If the full scale is to be shown
if(radial_scale==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])==length(r_object$data[,3])){
MINCILIM<-min(sin(atan(r_object$IVW.confint[1]))*R.IVW + Label.Scaling,sin(atan(r_object$egger.confint[1]-1))*(R.Egger +Label.Scaling_Egg-r_object$egger.coef[1,1]),r_object$egger.coef[1,1])
MAXCILIM<-max(sin(atan(r_object$IVW.confint[2]))*R.IVW + Label.Scaling,sin(atan(r_object$egger.confint[2]+1))*(R.Egger +Label.Scaling_Egg-r_object$egger.coef[1,1]),r_object$egger.coef[1,1])
if(min(r_object$data[,3]) < MINCILIM){
Y_MIN<-min(r_object$data[,3])
}
if(min(r_object$data[,3]) > MINCILIM){
Y_MIN<-MINCILIM
}
if(max(r_object$data[,3]) >MAXCILIM){
Y_MAX<-max(r_object$data[,3])
}
if(max(r_object$data[,3]) <MAXCILIM){
Y_MAX<-MAXCILIM
}
Y_Range<-Y_MAX-Y_MIN
#Generate a plot showing the MR-Egger and IVW estimates, showing all variants and not using a full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=Outliers)) +geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+
r_object$egger.coef[1,1],colour="MR-Egger"))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+scale_color_manual(breaks=c("Variant","Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="#000000","Outlier"="#E69F00"))+
theme(legend.title=element_blank())
#Indicate that no outliers are present
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])<length(r_object$data[,3])){
temp.dat<-r_object$data[unique(c(which(grepl("Outlier", r_object$egger.data[,6])),
which(grepl("Outlier", r_object$data[,6])))), ]
#Redefine IVW, MR-Egger and scale radii
maximal<-atan(max(abs(temp.dat[,3]))/max(abs(temp.dat[,2])))
R.All<-max(abs(r_object$data[,3]- r_object$egger.coef[1,1]))/sin(maximal)+median(r_object$data[,2])
R.IVW<-R.All+(R.All/12)
R.Egger<-R.All+(R.All/4)
#Redefine general label scaling parameter
Label.Scaling<-R.IVW/24
#Redefine MR-Egger label scaling parameter
Label.Scaling_Egg<-R.Egger/8
#Redefine values for plotting IVW, MR-Egger and scale circles
circledat_EGGEREST <- circle.radial(c(0, r_object$egger.coef[1,1]),R.Egger,length(temp.dat[,3]),atan(r_object$egger.confint[1]),atan(r_object$egger.confint[2]))
cxEgger<-circledat_EGGEREST$x
cyEgger<-circledat_EGGEREST$y
#Plot circle for overall scale
circledat_ALLEST <- circle.radial(c(0,0),R.All,length(temp.dat[,3]),atan(Scalemin),atan(Scalemax))
cxAll<-circledat_ALLEST$x
cyAll<-circledat_ALLEST$y
circledat_IVWEST <- circle.radial(c(0,0),R.IVW,length(temp.dat[,3]),atan(r_object$IVW.confint[1]),atan(r_object$IVW.confint[2]))
cxIVW<-circledat_IVWEST$x
cyIVW<-circledat_IVWEST$y
MINCILIM<-min(sin(atan(r_object$IVW.confint[1]))*R.IVW + Label.Scaling,sin(atan(r_object$egger.confint[1]-1))*(R.Egger +Label.Scaling_Egg-r_object$egger.coef[1,1]),r_object$egger.coef[1,1])
MAXCILIM<-max(sin(atan(r_object$IVW.confint[2]))*R.IVW + Label.Scaling,sin(atan(r_object$egger.confint[2]+1))*(R.Egger +Label.Scaling_Egg-r_object$egger.coef[1,1]),r_object$egger.coef[1,1])
if(min(temp.dat[,3]) < MINCILIM){
Y_MIN<-min(temp.dat[,3])
}
if(min(temp.dat[,3]) > MINCILIM){
Y_MIN<-MINCILIM
}
if(max(temp.dat[,3]) >MAXCILIM){
Y_MAX<-max(temp.dat[,3])
}
if(max(temp.dat[,3]) <MAXCILIM){
Y_MAX<-MAXCILIM
}
Y_Range<-Y_MAX-Y_MIN
#Generate a plot showing both IVW and MR-Egger estimates, only showing outlying variants and not using the full scale
B<-ggplot(temp.dat,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=out_types)) +geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+theme_bw() +
theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+r_object$egger.coef[1,1],colour="MR-Egger"))+
scale_y_continuous(limits = c(Y_MIN,Y_MAX))+scale_color_manual(breaks=c("IVW and MR-Egger Outlier","MR-Egger Outlier","IVW Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="white","IVW and MR-Egger Outlier"="#CC79A7","MR-Egger Outlier"="#E69F00","IVW Outlier"="#009E73"))+ theme(legend.title=element_blank())
#Draw lines showing Q statistic contributions for each variant using respective colours
for(i in 1:length(temp.dat[,3])){
if(abs((temp.dat[,3][i]-temp.dat[,2][i]*r_object$IVW.coef[1]))>abs((temp.dat[,3][i]-(temp.dat[,2][i]*r_object$egger.coef[2,1]+r_object$egger.coef[1,1])))){
B<- B + geom_segment(x = temp.dat[,2][i], xend = temp.dat[,2][i], y = temp.dat[,3][i], yend =temp.dat[,2][i]*r_object$IVW.coef[1],linetype="solid",colour="#56B4E9")
B<- B + geom_segment(x = temp.dat[,2][i], xend = temp.dat[,2][i], y = temp.dat[,3][i], yend =temp.dat[,2][i]*r_object$egger.coef[2,1]+r_object$egger.coef[1,1],linetype="solid",colour="#D55E00")
}
if(abs((temp.dat[,3][i]-temp.dat[,2][i]*r_object$IVW.coef[1]))<abs((temp.dat[,3][i]-(temp.dat[,2][i]*r_object$egger.coef[2,1]+r_object$egger.coef[1,1])))){
B<- B + geom_segment(x = temp.dat[,2][i], xend = temp.dat[,2][i], y = temp.dat[,3][i], yend =temp.dat[,2][i]*r_object$egger.coef[2,1]+r_object$egger.coef[1,1],linetype="solid",colour="#D55E00")
B<- B + geom_segment(x = temp.dat[,2][i], xend = temp.dat[,2][i], y = temp.dat[,3][i], yend =temp.dat[,2][i]*r_object$IVW.coef[1],linetype="solid",colour="#56B4E9")
}
}
}
}
}
#If only outliers are to be shown
if(show_outliers==FALSE){
#If the full scale is to be shown
if(radial_scale==TRUE){
#If axes scales should be fixed
if(scale_match==TRUE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])==length(r_object$data[,3])){
#Generate a plot showing both IVW and MR-Egger estimates, using the full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour="Variant"))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+coord_fixed()+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+
r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="#000000"))+ theme(legend.title=element_blank())
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])<length(r_object$data[,3])){
#Generates a plot showing the MR-Egger and IVW estimates, showing only outliers and using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=out_types))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+coord_fixed()+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW and MR-Egger Outlier","MR-Egger Outlier","IVW Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="black","IVW and MR-Egger Outlier"="#CC79A7","MR-Egger Outlier"="#E69F00","IVW Outlier"="#009E73"))+ theme(legend.title=element_blank())
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw individual ratio estimate lines for each outlier and Q distance indicator lines
Theta<-rep(0,length(r_object$data[,3]))
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
}
}
#If axes scales should be fixed
if(scale_match==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])==length(r_object$data[,3])){
#Generate a plot showing both IVW and MR-Egger estimates, using the full scale and all variants
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour="Variant"))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+
r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="#000000"))+ theme(legend.title=element_blank())
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])<length(r_object$data[,3])){
#Generates a plot showing the MR-Egger and IVW estimates, showing only outliers and using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=out_types))+geom_path(aes(x=cxAll,y=cyAll))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW and MR-Egger Outlier","MR-Egger Outlier","IVW Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="black","IVW and MR-Egger Outlier"="#CC79A7","MR-Egger Outlier"="#E69F00","IVW Outlier"="#009E73"))+ theme(legend.title=element_blank())
if(max(abs(r_object$data[,3]/r_object$data[,2]))>2){
Y_Scale<-Y_Range/6
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
if(max(abs(r_object$data[,3]/r_object$data[,2]))<2){
Y_Scale<-Y_Range/4
Y_Scale<-seq(from=Scalemin,to=Scalemax,by=Y_Scale)
Y_Scale<-c(Y_Scale,0)
Y_Scale<-mround(Y_Scale)
Y_Scale<-unique(Y_Scale)
for (i in 1:length(Y_Scale)){
B<- B + geom_text(x=(cos(atan(Y_Scale[i]))*(R.All+Label.Scaling)), y=(sin(atan(Y_Scale[i]))*(R.All+Label.Scaling)), label=Y_Scale[i],size=2.5)
}
}
#Draw individual ratio estimate lines for each outlier and Q distance indicator lines
Theta<-rep(0,length(r_object$data[,3]))
for(i in 1:length(r_object$data[,3])){
Theta<-atan(r_object$data[,3]/r_object$data[,2])
b<-sin(Theta)*R.All
a<-cos(Theta)*R.All
B<- B + geom_segment(x = 0, xend = a[i], y = 0, yend =b[i],linetype="dotted",colour="grey75")
}
}
}
}
#If the full scale is to be shown
if(radial_scale==FALSE){
#If no outliers are present
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])==length(r_object$data[,3])){
MINCILIM<-min(sin(atan(r_object$IVW.confint[1]))*R.IVW + Label.Scaling,sin(atan(r_object$egger.confint[1]-1))*(R.Egger +Label.Scaling_Egg-r_object$egger.coef[1,1]),r_object$egger.coef[1,1])
MAXCILIM<-max(sin(atan(r_object$IVW.confint[2]))*R.IVW + Label.Scaling,sin(atan(r_object$egger.confint[2]+1))*(R.Egger +Label.Scaling_Egg-r_object$egger.coef[1,1]),r_object$egger.coef[1,1])
if(min(r_object$data[,3]) < MINCILIM){
Y_MIN<-min(r_object$data[,3])
}
if(min(r_object$data[,3]) > MINCILIM){
Y_MIN<-MINCILIM
}
if(max(r_object$data[,3]) >MAXCILIM){
Y_MAX<-max(r_object$data[,3])
}
if(max(r_object$data[,3]) <MAXCILIM){
Y_MAX<-MAXCILIM
}
Y_Range<-Y_MAX-Y_MIN
#Generate a plot showing the MR-Egger and IVW estimates, showing all variants and not using a full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=Outliers)) +geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+
geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+
r_object$egger.coef[1,1],colour="MR-Egger"))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+scale_color_manual(breaks=c("Variant","Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="#000000","Outlier"="#E69F00"))+
theme(legend.title=element_blank())
#Indicate that no outliers are present
print("No significant Outliers")
}
if(nrow(r_object$data[r_object$data$out_types == "Variant", ])<length(r_object$data[,3])){
#Generates a plot showing the MR-Egger and IVW estimates, showing only outliers and using the full scale
B<-ggplot(r_object$data,aes(x=Wj,y=BetaWj)
)+labs(title="Radial Estimates")+ geom_point(aes(colour=out_types))+geom_path(aes(x=cxIVW,y=cyIVW,colour="IVW"))+
geom_text(x=cos(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), y=sin(atan(r_object$IVW.coef[1]))*(R.IVW+Label.Scaling*1.5), label=round(r_object$IVW.coef[1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[1])-0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),y=sin(atan(r_object$IVW.confint[2])+0.02)*(R.IVW+Label.Scaling),label=round(r_object$IVW.confint[2],digits=3),size=3)+
theme_bw() +theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"))+ylab(expression(hat(beta)[j]~sqrt(W[j])))+xlab(expression(sqrt(W[j])))+geom_segment(aes(x = 0, xend = cos(atan(r_object$IVW.coef[1]))*R.IVW, y = 0, yend = sin(atan(r_object$IVW.coef[1]))*R.IVW,colour="IVW"))+
scale_x_continuous(limits = c(0,max(cxEgger)+Label.Scaling_Egg*2),expand=c(0,0))+scale_y_continuous(limits = c(Y_MIN,Y_MAX))+
geom_path(aes(x=cxEgger,y=cyEgger,colour="MR-Egger"))+
geom_text(x=cos(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5), y=sin(atan(r_object$egger.coef[2,1]))*(R.Egger+Label.Scaling*1.5) +r_object$egger.coef[1,1],label=round(r_object$egger.coef[2,1],digits=3),size=4)+
geom_text(x=cos(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[1]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[1],digits=3),size=3)+
geom_text(x=cos(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5),y=(sin(atan(r_object$egger.confint[2]))*(R.Egger+Label.Scaling*1.5))+r_object$egger.coef[1,1],label=round(r_object$egger.confint[2],digits=3),size=3)+
geom_segment(aes(x = 0, xend = cos(atan(r_object$egger.coef[2,1]))*R.Egger, y = r_object$egger.coef[1,1], yend = (sin(atan(r_object$egger.coef[2,1]))*R.Egger)+r_object$egger.coef[1,1],colour="MR-Egger"))+scale_color_manual(breaks=c("Variant","IVW and MR-Egger Outlier","MR-Egger Outlier","IVW Outlier","IVW","MR-Egger"),values=c("IVW"="#56B4E9","MR-Egger"="#D55E00","Variant"="black","IVW and MR-Egger Outlier"="#CC79A7","MR-Egger Outlier"="#E69F00","IVW Outlier"="#009E73"))+ theme(legend.title=element_blank())
}
}
}
}
return(B)
}
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