R/ggSpine.R
In cardiomoon/ggiraphExtra: Make Interactive 'ggplot2'. Extension to 'ggplot2' and 'ggiraph'
Defines functions
my_summarize_n
my_sumSub
num2cutData
#'Draw an interactive spinogram
#'
#'@param data A data.frame
#'@param mapping Set of aesthetic mappings created by aes or aes_.
#'@param stat The statistical transformation to use on the data for this layer, as a string
#' c("count","identity")
#'@param position Position adjustment. One of the c("fill","stack","dodge")
#'@param palette A character string indicating the color palette
#'@param interactive A logical value. If TRUE, an interactive plot will be returned
#'@param polar A logical value. If TRUE, coord_polar() function will be added
#'@param reverse If true, reverse palette colors
#'@param width Bar width
#'@param maxylev integer indicating threshold of unique value to be treated as a categorical variable
#'@param digits integer indicating the number of decimal places
#'@param colour Bar colour
#'@param size Bar size
#'@param addlabel A logical value. If TRUE, label will be added to the plot
#'@param labelsize label size
#'@param minlabelgroup minimal threshold of label group. Default is 0.04
#'@param minlabel minimal threshold of label. Default is 2
#'@param hide.legend A logical value. If TRUE, the legend is removed and y labels are recreated
#'@param ylabelMean Logical. If TRUE, y axis labels are positioned at mean value.
#'@param sec.y.axis Logical. If TRUE, secondary y axis is shown at the right side.
#'@param use.label Logical. Whether or not use column label in case of labelled data
#'@param use.labels Logical. Whether or not use value labels in case of labelled data
#'@param labeller A function that takes one data frame of labels and returns a list or data frame of character vectors.
#'@param facetbycol Logical. If TRUE, facet by column.
#'@param xangle angle of axis label
#'@param yangle angle of axis label
#'@param xreverse Logical. Whether or not reverse x-axis
#'@param yreverse Logical. Whether or not reverse y-axis
#'@param xlab Label for x-axis
#'@param filllab Label for fill aes
#'@param family font family
#'@param ... other arguments passed on to geom_rect_interactive.
#'@importFrom ggplot2 coord_polar scale_y_continuous guide_legend sec_axis scale_x_reverse scale_y_reverse
#'@importFrom ggiraph geom_rect_interactive
#'@importFrom dplyr lag group_by n
#'@importFrom magrittr '%>%'
#'@importFrom scales percent
#'@importFrom tidyr spread complete
#'@importFrom dplyr select arrange
#'@importFrom plyr '.'
#'@importFrom purrr map_df
#'@export
#'@return An interactive spinogram
#'@examples
#'require(moonBook)
#'require(ggplot2)
#'acs$Dx=factor(acs$Dx,levels=c("Unstable Angina","NSTEMI","STEMI"))
#'ggSpine(data=acs,aes(x=age,fill=Dx,facet=sex),palette="Reds")
#'ggSpine(data=acs,aes(x=age,fill=Dx,facet=sex),facetbycol=FALSE,minlabelgroup=0.02)
#'ggSpine(data=acs,aes(x=age,fill=Dx),palette="Reds")
#'ggSpine(data=acs,aes(x=smoking,fill=Dx),palette="Reds")
#'ggSpine(data=acs,aes(x=DM,fill=Dx,facet=sex),palette="Reds")
#'ggSpine(data=acs,aes(x=Dx,fill=smoking,facet=sex),palette="Reds")
#'ggSpine(data=acs,aes(x=DM,facet=smoking,fill=Dx),sec.y.axis=TRUE)
#'ggSpine(data=acs,aes(x=DM,facet=smoking,fill=Dx),facetbycol=FALSE)
#'ggSpine(mtcars,aes(x=gear,fill=carb),interactive=TRUE)
#'ggSpine(mtcars,aes(x=gear,fill=carb,facet=am))
#'ggSpine(data=acs,aes(x=Dx,fill=smoking),position="dodge")
#'ggSpine(data=acs,aes(x=Dx,fill=smoking),position="stack")
ggSpine=function (data, mapping, stat = "count", position = "fill", palette = "Blues",
interactive = FALSE, polar = FALSE, reverse = FALSE, width = NULL,maxylev=6,
digits = 1, colour = "black", size = 0.2, addlabel = TRUE, labelsize=5,
minlabelgroup=0.04,minlabel=2,
hide.legend=TRUE,ylabelMean=FALSE,sec.y.axis=FALSE,
use.label=TRUE,use.labels=TRUE,labeller=NULL,facetbycol=TRUE,
xangle=NULL,yangle=NULL, xreverse=FALSE, yreverse=FALSE,
xlab=NULL,filllab=NULL,family=NULL,...)
{
# data=mtcars;mapping=aes(x=gear,fill=carb,facet=am)
# stat = "count"; position = "fill"; palette = "Blues"
# interactive = FALSE; polar = FALSE; reverse = FALSE; width = NULL;maxylev=6
# digits = 1; colour = "black"; size = 0.2; addlabel = TRUE; labelsize=5
# minlabelgroup=0.04;minlabel=2
# hide.legend=TRUE;ylabelMean=FALSE;sec.y.axis=FALSE
# use.label=TRUE;use.labels=TRUE;labeller=NULL;facetbycol=TRUE
# xangle=NULL;yangle=NULL
#
# data=acs;mapping=aes(x=DM,fill=Dx,facet=sex)
# palette="Reds";addlabel=TRUE
# stat = "count"; position = "fill"; palette = "Blues";
# interactive = FALSE; polar = FALSE; reverse = FALSE; width = NULL;maxylev=6
# digits = 1; colour = "black"; size = 0.2; addlabel = FALSE; hide.legend=TRUE
# use.label=TRUE;use.labels=TRUE;labeller=NULL;facetbycol=TRUE;sec.y.axis=FALSE
# xangle=NULL;yangle=NULL;minlabelgroup=0.04;minlabel=2;labelsize=5;ylabelMean=FALSE
# df=mtcars %>% group_by(gear,carb,am) %>% summarize(n=n())
# ggSpine(df,aes(x=gear,fill=carb,y=n,facet=am),stat="identity")
# data=df;mapping=aes(x=name,fill=group,y=rate);stat="identity"
# xreverse=FALSE;yreverse=FALSE
# data
# require(scales)
# require(purrr)
# require(tidyverse)
xvar <- fillvar <- facetvar <- yvar <- NULL
if ("x" %in% names(mapping))
xvar <- getMapping(mapping,"x")
if ("y" %in% names(mapping))
yvar <- getMapping(mapping,"y")
if ("fill" %in% names(mapping))
fillvar <- getMapping(mapping,"fill")
if ("facet" %in% names(mapping))
facetvar <- getMapping(mapping,"facet")
contmode = 0
if(is.null(xlab)){
(xlab=attr(data[[xvar]],"label"))
if(is.null(xlab)) xlab=xvar
if(!use.label) xlab=xvar
}
if(is.null(filllab)){
(filllab=attr(data[[fillvar]],"label"))
if(is.null(filllab)) filllab=fillvar
if(!use.label) filllab=fillvar
}
if(use.labels) data=addLabelDf(data,mapping=mapping)
if (is.numeric(data[[xvar]])&(length(unique(data[[xvar]]))>maxylev)) {
if (is.null(width)) width = 1
width
contmode = 1
if(is.null(facetvar)){
df2<-num2cutData(data,xvar,fillvar,width,position,digits,facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
} else{
df1<-data %>% split(.[[`facetvar`]]) %>%
lapply(num2cutData,xvar,fillvar,width,position,digits,facetbycol,
minlabelgroup,minlabel)
for(i in 1:length(df1)) {
df1[[i]][[facetvar]]=names(df1)[[i]]
}
df2<-map_df(df1,rbind)
}
if(is.factor(data[[fillvar]])){
df2[[fillvar]]=factor(df2[[fillvar]],levels=levels(data[[fillvar]]))
}
} else if ((stat == "identity") & (!is.null(yvar))) {
if(is.null(width)) width=0.9
# data<-mtcars%>% group_by(gear,carb,am) %>% summarize(n=n())
# mapping=aes(facet=am,fill=gear,y=n,x=carb)
# position="fill";digits=1;facetbycol=TRUE;facetvar="am";width=0.9
data=data.frame(data)
data
if(!is.null(facetvar)){
data<-data %>% complete(!!mapping$x,!!mapping$fill,!!mapping$facet)
data[[yvar]][is.na(data[[yvar]])]=0
data=data.frame(data)
}
my_summarize_n2=function(data,mapping,width,position,digits,facetbycol,minlabelgroup,minlabel){
# df=acs %>% group_by(Dx,sex) %>% summarize(n=n())
# data=df;mapping=aes(x=Dx,fill=sex,y=n);stat="identity"
# position="fill";digits=1;facetbycol=TRUE;width=0.9;minlabelgroup=0.04;minlabel=2
df = data %>%
select(!!mapping$x,!!mapping$fill,!!mapping$y) %>%
arrange(!!mapping$x,!!mapping$fill)
df
colnames(df)[ncol(df)] = "n"
df=data.frame(df)
df <- df %>% complete(!!mapping$x,!!mapping$fill,fill=list(n=0))
df
df1 <- df %>% tidyr::spread(!!mapping$x,n)
df1
# df =df[order(df[[xvar]],df[[fillvar]]),]
# colnames(df)[3] = "n"
#
# df1<-df %>% spread(!!mapping$x,n)
df1=data.frame(df1)
rownames(df1)=df1[[1]]
df1<-df1[-1]
a=as.matrix(df1)
a
my_sumSub(df,a,width=width,position=position,digits=digits,facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
}
if(is.null(facetvar)){
df2=my_summarize_n2(data,mapping,width,position,digits,facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
} else{
df1<-data %>% split(.[[`facetvar`]]) %>%
lapply(my_summarize_n2,mapping,width,position,digits,facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
for(i in 1:length(df1)) {
df1[[i]][[facetvar]]=names(df1)[[i]]
}
df2<-map_df(df1,rbind)
df2
}
} else {
if(is.null(width)) width=0.9
if(is.null(facetvar)){
df2=my_summarize_n(data,mapping,
width=width,position=position,digits=digits,facetbycol=facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
} else{
if(!is.factor(data[[fillvar]])) data[[fillvar]]=factor(data[[fillvar]])
# str(data)
df1<-data %>% split(.[[`facetvar`]]) %>%
lapply(my_summarize_n,mapping,
width=width,position=position,digits=digits,facetbycol=facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
df1
for(i in 1:length(df1)) {
df1[[i]][[facetvar]]=names(df1)[[i]]
}
df2<-map_df(df1,rbind)
df3<-df2 %>%complete(!!mapping$fill,fill=list(n=0,ratio=0,label=""))
df3<-data.frame(df3)
df3
}
df2
}
xlabels = levels(factor(df2[[1]]))
xlabels
ylabels = levels(factor(data[[fillvar]]))
ylabels
if (contmode) {
total=nrow(data)
ycount = length(ylabels)
(pos = 1:ycount)
y = (100/ycount) * (pos - 1) + (100/ycount)/2
if(facetbycol==FALSE) y=y*(total/100)
} else {
if(ylabelMean){
y=rowMeans(matrix(df2$y,nrow=length(ylabels)))
} else{
df2
if(is.null(facetvar)){
y=df2$y[df2$xno==1]
y[which(df2$ratio[df2$xno==1]==0)]=NA
yend=df2$y[df2$xno==max(df2$xno)]
yend[which(df2$ratio[df2$xno==max(df2$xno)]==0)]=NA
if(xreverse){
ytemp=y
y=yend
yend=ytemp
}
if(any(is.na(y))) sec.y.axis=TRUE
} else{
condition=(df2$xno==1)&(df2[[facetvar]]==unique(df2[[facetvar]])[1])
y=df2$y[condition]
y[which(df2$ratio[condition]==0)]=NA
condition1=(df2$xno==max(df2$xno))&
(df2[[facetvar]]==unique(df2[[facetvar]])[length(unique(df2[[facetvar]]))])
yend=df2$y[condition1]
yend[which(df2$ratio[condition1]==0)]=NA
if(xreverse){
ytemp=y
y=yend
yend=ytemp
}
if(any(is.na(y))) sec.y.axis=TRUE
}
}
}
if(!is.null(facetvar)){
if(facetbycol==FALSE) hide.legend=FALSE
}
if (is.numeric(df2[[fillvar]]))
df2[[fillvar]] = factor(df2[[fillvar]])
df2
p <- ggplot(mapping = aes_string(xmin = "xmin", xmax = "xmax",
ymin = "ymin", ymax = "ymax", fill = fillvar), data = df2)
p <- p +geom_rect_interactive(aes_string(tooltip = "tooltip",
data_id = "data_id"), size = size, colour = colour,...)
# p <- p +geom_rect_interactive(aes_string(tooltip = "tooltip",
# data_id = "data_id"), size = size, colour = colour)
# p
if(!is.null(facetvar)) {
addNumber<-function(string){
if ((stat == "identity") & (!is.null(yvar))){
result=sapply(string,function(x){paste0(facetvar,":",x,"\nN=",
sum(data[data[[facetvar]]==x,"n"]) )})
} else{
result=sapply(string,function(x){paste0(facetvar,":",x,"\nN=",nrow(data[data[[facetvar]]==x,]))})
}
result
}
if(is.null(labeller)){
if(facetbycol){
p<-p+eval(parse(text=paste0("facet_grid(.~",facetvar,",scales='free_x',space='free',labeller=labeller(.default=addNumber))")))
} else{
p<-p+eval(parse(text=paste0("facet_grid(",facetvar,"~.,scales='free_y',space='free_y',switch='y',labeller=labeller(.default=addNumber))")))
}
} else{
if(facetbycol){
p<-p+eval(parse(text=paste0("facet_grid(.~",facetvar,",scales='free_x',space='free',labeller=",labeller,")")))
} else{
p<-p+eval(parse(text=paste0("facet_grid(",facetvar,"~.,scales='free_y',space='free_y',switch='y',labeller=",labeller,")")))
}
}
}
p
# x=rowMeans(matrix(unique(df2$x),nrow=length(xlabels)))
# if (contmode) {
# p <- p + scale_x_continuous(breaks = xmax, labels = xlabels,name=xlab,
# limits = c(0, total))
# }else {
# #if(length(x)!=length(xlabels)) xlabels=c(xlabels,NA)
# p<-p + scale_x_continuous(breaks = NULL, labels = NULL, name=xlab)
# }
if(!is.null(facetvar)) p<-p + scale_x_continuous(breaks = NULL, labels = NULL, name=xlab)
direction = ifelse(reverse, -1, 1)
if ((position != "dodge") & hide.legend ){
if(sec.y.axis){
if(yreverse){
p <- p + scale_y_reverse(breaks = y, labels = ylabels,name=filllab,
sec.axis=sec_axis(trans=~.,breaks = yend, labels = ylabels,name=filllab))
} else{
p <- p + scale_y_continuous(breaks = y, labels = ylabels,name=filllab,
sec.axis=sec_axis(trans=~.,breaks = yend, labels = ylabels,name=filllab))
}
} else{
if(yreverse){
p<-p + scale_y_reverse(breaks = y, labels = ylabels,name=filllab)
} else{
p<-p + scale_y_continuous(breaks = y, labels = ylabels,name=filllab)
}
}
p<- p+ scale_fill_brewer(palette = palette, direction = direction,
guide = FALSE) + ylab("")
} else{
p <- p + ylab("count")+guides(fill=guide_legend(reverse=TRUE))
p <- p + scale_fill_brewer(palette = palette,
direction = direction)
}
p
if (addlabel)
p = p + geom_text(aes_string(x = "x", y = "y", label = "label"),size=labelsize)
if(is.null(xangle)){
if(max(nchar(colnames(df2)))>10) xangle=20
else xangle=0
}
p<-p+theme(axis.text.x=element_text(angle=xangle,vjust = 0.5))
p
if(is.null(yangle)) yangle=90
p <- p + theme(axis.text.y = element_text(angle = yangle),
axis.text.y.right = element_text(angle = -yangle),
axis.ticks.y = element_blank())
df3=df2[df2$yno==1,]
vjust=ifelse(facetbycol,1.8,1)
if(yreverse) vjust=ifelse(facetbycol,-1,-0.1)
if(contmode){
total=nrow(data)
df3
df3$ratio1=df3$width/total
df3$label=stringr::str_extract(substr(df3[[xvar]],2,nchar(df3[[xvar]])),"^[^,]+")
if(mean(as.numeric(df3$label))>1e+9) {
df3$label=paste0(as.numeric(df3$label)/1e+9,"T")
} else if(mean(as.numeric(df3$label))>1e+6) {
df3$label=paste0(as.numeric(df3$label)/1e+6,"M")
} else if(mean(as.numeric(df3$label))>1e+3) {
df3$label=paste0(as.numeric(df3$label)/1e+3,"K")
}
df3$ratio2=lag(df3$ratio1)
df3$ratio2[1]=df3$ratio1[1]
df3$label[(df3$ratio1<minlabelgroup)&(df3$ratio2<minlabelgroup)]=""
p
if(is.null(facetvar)){
if(xreverse){
p<-p + scale_x_reverse(breaks = df3$xmin,labels = df3$label,name=xlab)
} else{
p<-p + scale_x_continuous(breaks = df3$xmin,labels = df3$label,name=xlab)
}
} else{
p<-p + geom_text(aes_string(x = "xmin", y = "0", label = "label"),data=df3,vjust=vjust)
}
} else{
if(is.null(facetvar)){
if(xreverse){
p<-p + scale_x_reverse(breaks = df3$x,labels = df3[[xvar]],name=xlab)
} else{
p<-p + scale_x_continuous(breaks = df3$x,labels = df3[[xvar]],name=xlab)
}
} else{
if(!is.factor(df3[[xvar]])) df3[[xvar]]=factor(df3[[xvar]])
df3$label2=ifelse(df3$ratio>=0,levels(df3[[xvar]]),"")
if(is.null(family)){
p<-p + geom_text(aes_string(x = "x", y = ifelse(yreverse,"100","0"), label = "label2"),
data=df3,vjust=vjust)
} else{
p<-p + geom_text(aes_string(x = "x", y = ifelse(yreverse,"100","0"), label = "label2"),
data=df3,vjust=vjust,family=family)
}
}
}
if(!is.null(family)) p<-p+theme(text= element_text(family=family))
if(facetbycol==FALSE){
if(yreverse){
p<-p + scale_y_reverse(breaks = NULL, labels = NULL,name=NULL)
} else{
p<-p + scale_y_continuous(breaks = NULL, labels = NULL,name=NULL)
}
p <- p + theme(legend.position="bottom")
}
p
if(!is.null(facetvar)) p<-p+theme(strip.placement = "outside")
if (polar == TRUE)
p <- p + coord_polar()
if (interactive){
tooltip_css <- "background-color:white;font-style:italic;padding:10px;border-radius:10px 20px 10px 20px;"
hover_css = "fill-opacity=.3;cursor:pointer;stroke:gold;"
p<-girafe(ggobj=p)
p<-girafe_options(p,
opts_hover(css=hover_css),
opts_tooltip(css=tooltip_css,opacity=.75),
opts_zoom(min=1,max=10))
}
p
}
num2cutData=function(data,xvar,fillvar,width=0.9,position="fill",digits=1,facetbycol=TRUE,
minlabelgroup=0.04,minlabel=2){
result = num2cut(data[[xvar]])
result
b = result$x1
breaks = result$breaks
a = table(data[[fillvar]], b)
a
df=as.data.frame(a,stringsAsFactors = FALSE)
# df = reshape2::melt(a)
df = df[c(2, 1, 3)]
colnames(df) = c(xvar, fillvar, "n")
df
a
my_sumSub(df,a,width=width,position=position,digits=digits,facetbycol=facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
}
my_sumSub=function(df,a,width=0.9,position="fill",digits=1,facetbycol=TRUE,minlabelgroup=0.04,minlabel=2){
# acs$Dx=factor(acs$Dx,levels=c("Unstable Angina","NSTEMI","STEMI"))
# df=acs %>% group_by(Dx,smoking) %>%summarize(n=n())
# a=table(acs$smoking,acs$Dx)
# width=0.9;position="fill";digits=1;facetbycol=TRUE;
# minlabelgroup=0.04,minlabel=2
#
# str(df)
# str(a)
(total = sum(a))
(csum = colSums(a))
(rsum = rowSums(a))
(xmax = cumsum(csum))
(xmin = cumsum(csum) - csum)
(x = (xmax + xmin)/2)
(width = csum * width)
(xmax = x + width/2)
(xmin = x - width/2)
df$xno=rep(1:ncol(a),each=nrow(a))
df$yno=rep(1:nrow(a),ncol(a))
df=as.data.frame(df)
df
df$csum = rep(csum,each=nrow(a))
df$xmin = rep(xmin,each=nrow(a))
df$xmax = rep(xmax,each=nrow(a))
df$x = rep(x,each=nrow(a))
df$width = rep(width,each=nrow(a))
count = max(df$xno,na.rm=TRUE)
df
count
if (position == "dodge") {
df$ymax = df$n
df$ymin = 0
df
df$y = (df$ymax + df$ymin)/2
ycount = max(df$yno,na.rm=TRUE)
df$xmin2 = df$xmin + (df$yno - 1) * (df$width/ycount)
df$xmax2 = df$xmin2 + (df$width/ycount)
df$xmin = df$xmin2
df$xmax = df$xmax2
df$x = (df$xmax + df$xmin)/2
df2 = df
} else {
for (i in 1:count) {
dfsub = df[df$xno == i, ]
dfsub$ratio = round(dfsub$n * 100/csum[i], digits)
dfsub$ymax = cumsum(dfsub$n)
dfsub$ymin = dfsub$ymax - dfsub$n
if (position == "fill") {
dfsub$ymax = dfsub$ymax * 100/csum[i]
dfsub$ymin = dfsub$ymin * 100/csum[i]
}
dfsub$y = (dfsub$ymin + dfsub$ymax)/2
if (i == 1) {
df2 = dfsub
} else {
df2 = rbind(df2, dfsub)
}
df2
}
}
df2$data_id = as.character(1:nrow(df2))
df2$tooltip = paste0(df2[[2]], "<br>", df2[[1]],
"<br>", df2$nrow)
df2$label = ifelse((df2$csum/total) >= minlabelgroup, df2$n, "")
df2$tooltip = paste0(df2$tooltip, "(", df2$ratio, "%)")
if (position == "fill") {
df2$label = ifelse((df2$csum/total) >= minlabelgroup,
ifelse(df2$ratio >= minlabel,percent(df2$ratio/100),""),"")
}
df2
if(facetbycol==FALSE){
df2$xmin=df2$xmin/total
df2$xmax=df2$xmax/total
df2$x=df2$x/total
df2$ymin=df2$ymin*(total/100)
df2$ymax=df2$ymax*(total/100)
df2$y=df2$y*(total/100)
}
df2
}
my_summarize_n=function(data,mapping,width=0.9,position="fill",digits=1,facetbycol=TRUE,
minlabelgroup=0.04,minlabel=2){
# data=mtcars;mapping=aes(x=carb,fill=gear)
# width=0.9;position="fill";digits=1;facetbycol=TRUE
# minlabelgroup=0.04;minlabel=2
#
# data[[mapping$fill]]=factor(data[[mapping$fill]])
#
# df<-data %>%
# group_by( !!mapping$x,!!mapping$fill) %>%
# dplyr::summarize(n=n()) %>%
# tidyr::complete(!!mapping$fill,fill=list(n=0))
# df=data.frame(df)
# df
xvar=getMapping(mapping,"x")
fillvar=getMapping(mapping,"fill")
a=table(data[[xvar]],data[[fillvar]])
df=data.frame(a)
colnames(df)=c(xvar,fillvar,"n")
df<-df %>% arrange(!!mapping$x,!!mapping$fill)
my_sumSub(df,t(a),width=width,position=position,digits=digits,facetbycol=facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
}
cardiomoon/ggiraphExtra documentation built on Oct. 9, 2020, 4:16 a.m.
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Defines functions my_summarize_n my_sumSub num2cutData
#'Draw an interactive spinogram
#'
#'@param data A data.frame
#'@param mapping Set of aesthetic mappings created by aes or aes_.
#'@param stat The statistical transformation to use on the data for this layer, as a string
#' c("count","identity")
#'@param position Position adjustment. One of the c("fill","stack","dodge")
#'@param palette A character string indicating the color palette
#'@param interactive A logical value. If TRUE, an interactive plot will be returned
#'@param polar A logical value. If TRUE, coord_polar() function will be added
#'@param reverse If true, reverse palette colors
#'@param width Bar width
#'@param maxylev integer indicating threshold of unique value to be treated as a categorical variable
#'@param digits integer indicating the number of decimal places
#'@param colour Bar colour
#'@param size Bar size
#'@param addlabel A logical value. If TRUE, label will be added to the plot
#'@param labelsize label size
#'@param minlabelgroup minimal threshold of label group. Default is 0.04
#'@param minlabel minimal threshold of label. Default is 2
#'@param hide.legend A logical value. If TRUE, the legend is removed and y labels are recreated
#'@param ylabelMean Logical. If TRUE, y axis labels are positioned at mean value.
#'@param sec.y.axis Logical. If TRUE, secondary y axis is shown at the right side.
#'@param use.label Logical. Whether or not use column label in case of labelled data
#'@param use.labels Logical. Whether or not use value labels in case of labelled data
#'@param labeller A function that takes one data frame of labels and returns a list or data frame of character vectors.
#'@param facetbycol Logical. If TRUE, facet by column.
#'@param xangle angle of axis label
#'@param yangle angle of axis label
#'@param xreverse Logical. Whether or not reverse x-axis
#'@param yreverse Logical. Whether or not reverse y-axis
#'@param xlab Label for x-axis
#'@param filllab Label for fill aes
#'@param family font family
#'@param ... other arguments passed on to geom_rect_interactive.
#'@importFrom ggplot2 coord_polar scale_y_continuous guide_legend sec_axis scale_x_reverse scale_y_reverse
#'@importFrom ggiraph geom_rect_interactive
#'@importFrom dplyr lag group_by n
#'@importFrom magrittr '%>%'
#'@importFrom scales percent
#'@importFrom tidyr spread complete
#'@importFrom dplyr select arrange
#'@importFrom plyr '.'
#'@importFrom purrr map_df
#'@export
#'@return An interactive spinogram
#'@examples
#'require(moonBook)
#'require(ggplot2)
#'acs$Dx=factor(acs$Dx,levels=c("Unstable Angina","NSTEMI","STEMI"))
#'ggSpine(data=acs,aes(x=age,fill=Dx,facet=sex),palette="Reds")
#'ggSpine(data=acs,aes(x=age,fill=Dx,facet=sex),facetbycol=FALSE,minlabelgroup=0.02)
#'ggSpine(data=acs,aes(x=age,fill=Dx),palette="Reds")
#'ggSpine(data=acs,aes(x=smoking,fill=Dx),palette="Reds")
#'ggSpine(data=acs,aes(x=DM,fill=Dx,facet=sex),palette="Reds")
#'ggSpine(data=acs,aes(x=Dx,fill=smoking,facet=sex),palette="Reds")
#'ggSpine(data=acs,aes(x=DM,facet=smoking,fill=Dx),sec.y.axis=TRUE)
#'ggSpine(data=acs,aes(x=DM,facet=smoking,fill=Dx),facetbycol=FALSE)
#'ggSpine(mtcars,aes(x=gear,fill=carb),interactive=TRUE)
#'ggSpine(mtcars,aes(x=gear,fill=carb,facet=am))
#'ggSpine(data=acs,aes(x=Dx,fill=smoking),position="dodge")
#'ggSpine(data=acs,aes(x=Dx,fill=smoking),position="stack")
ggSpine=function (data, mapping, stat = "count", position = "fill", palette = "Blues",
interactive = FALSE, polar = FALSE, reverse = FALSE, width = NULL,maxylev=6,
digits = 1, colour = "black", size = 0.2, addlabel = TRUE, labelsize=5,
minlabelgroup=0.04,minlabel=2,
hide.legend=TRUE,ylabelMean=FALSE,sec.y.axis=FALSE,
use.label=TRUE,use.labels=TRUE,labeller=NULL,facetbycol=TRUE,
xangle=NULL,yangle=NULL, xreverse=FALSE, yreverse=FALSE,
xlab=NULL,filllab=NULL,family=NULL,...)
{
# data=mtcars;mapping=aes(x=gear,fill=carb,facet=am)
# stat = "count"; position = "fill"; palette = "Blues"
# interactive = FALSE; polar = FALSE; reverse = FALSE; width = NULL;maxylev=6
# digits = 1; colour = "black"; size = 0.2; addlabel = TRUE; labelsize=5
# minlabelgroup=0.04;minlabel=2
# hide.legend=TRUE;ylabelMean=FALSE;sec.y.axis=FALSE
# use.label=TRUE;use.labels=TRUE;labeller=NULL;facetbycol=TRUE
# xangle=NULL;yangle=NULL
#
# data=acs;mapping=aes(x=DM,fill=Dx,facet=sex)
# palette="Reds";addlabel=TRUE
# stat = "count"; position = "fill"; palette = "Blues";
# interactive = FALSE; polar = FALSE; reverse = FALSE; width = NULL;maxylev=6
# digits = 1; colour = "black"; size = 0.2; addlabel = FALSE; hide.legend=TRUE
# use.label=TRUE;use.labels=TRUE;labeller=NULL;facetbycol=TRUE;sec.y.axis=FALSE
# xangle=NULL;yangle=NULL;minlabelgroup=0.04;minlabel=2;labelsize=5;ylabelMean=FALSE
# df=mtcars %>% group_by(gear,carb,am) %>% summarize(n=n())
# ggSpine(df,aes(x=gear,fill=carb,y=n,facet=am),stat="identity")
# data=df;mapping=aes(x=name,fill=group,y=rate);stat="identity"
# xreverse=FALSE;yreverse=FALSE
# data
# require(scales)
# require(purrr)
# require(tidyverse)
xvar <- fillvar <- facetvar <- yvar <- NULL
if ("x" %in% names(mapping))
xvar <- getMapping(mapping,"x")
if ("y" %in% names(mapping))
yvar <- getMapping(mapping,"y")
if ("fill" %in% names(mapping))
fillvar <- getMapping(mapping,"fill")
if ("facet" %in% names(mapping))
facetvar <- getMapping(mapping,"facet")
contmode = 0
if(is.null(xlab)){
(xlab=attr(data[[xvar]],"label"))
if(is.null(xlab)) xlab=xvar
if(!use.label) xlab=xvar
}
if(is.null(filllab)){
(filllab=attr(data[[fillvar]],"label"))
if(is.null(filllab)) filllab=fillvar
if(!use.label) filllab=fillvar
}
if(use.labels) data=addLabelDf(data,mapping=mapping)
if (is.numeric(data[[xvar]])&(length(unique(data[[xvar]]))>maxylev)) {
if (is.null(width)) width = 1
width
contmode = 1
if(is.null(facetvar)){
df2<-num2cutData(data,xvar,fillvar,width,position,digits,facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
} else{
df1<-data %>% split(.[[`facetvar`]]) %>%
lapply(num2cutData,xvar,fillvar,width,position,digits,facetbycol,
minlabelgroup,minlabel)
for(i in 1:length(df1)) {
df1[[i]][[facetvar]]=names(df1)[[i]]
}
df2<-map_df(df1,rbind)
}
if(is.factor(data[[fillvar]])){
df2[[fillvar]]=factor(df2[[fillvar]],levels=levels(data[[fillvar]]))
}
} else if ((stat == "identity") & (!is.null(yvar))) {
if(is.null(width)) width=0.9
# data<-mtcars%>% group_by(gear,carb,am) %>% summarize(n=n())
# mapping=aes(facet=am,fill=gear,y=n,x=carb)
# position="fill";digits=1;facetbycol=TRUE;facetvar="am";width=0.9
data=data.frame(data)
data
if(!is.null(facetvar)){
data<-data %>% complete(!!mapping$x,!!mapping$fill,!!mapping$facet)
data[[yvar]][is.na(data[[yvar]])]=0
data=data.frame(data)
}
my_summarize_n2=function(data,mapping,width,position,digits,facetbycol,minlabelgroup,minlabel){
# df=acs %>% group_by(Dx,sex) %>% summarize(n=n())
# data=df;mapping=aes(x=Dx,fill=sex,y=n);stat="identity"
# position="fill";digits=1;facetbycol=TRUE;width=0.9;minlabelgroup=0.04;minlabel=2
df = data %>%
select(!!mapping$x,!!mapping$fill,!!mapping$y) %>%
arrange(!!mapping$x,!!mapping$fill)
df
colnames(df)[ncol(df)] = "n"
df=data.frame(df)
df <- df %>% complete(!!mapping$x,!!mapping$fill,fill=list(n=0))
df
df1 <- df %>% tidyr::spread(!!mapping$x,n)
df1
# df =df[order(df[[xvar]],df[[fillvar]]),]
# colnames(df)[3] = "n"
#
# df1<-df %>% spread(!!mapping$x,n)
df1=data.frame(df1)
rownames(df1)=df1[[1]]
df1<-df1[-1]
a=as.matrix(df1)
a
my_sumSub(df,a,width=width,position=position,digits=digits,facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
}
if(is.null(facetvar)){
df2=my_summarize_n2(data,mapping,width,position,digits,facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
} else{
df1<-data %>% split(.[[`facetvar`]]) %>%
lapply(my_summarize_n2,mapping,width,position,digits,facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
for(i in 1:length(df1)) {
df1[[i]][[facetvar]]=names(df1)[[i]]
}
df2<-map_df(df1,rbind)
df2
}
} else {
if(is.null(width)) width=0.9
if(is.null(facetvar)){
df2=my_summarize_n(data,mapping,
width=width,position=position,digits=digits,facetbycol=facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
} else{
if(!is.factor(data[[fillvar]])) data[[fillvar]]=factor(data[[fillvar]])
# str(data)
df1<-data %>% split(.[[`facetvar`]]) %>%
lapply(my_summarize_n,mapping,
width=width,position=position,digits=digits,facetbycol=facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
df1
for(i in 1:length(df1)) {
df1[[i]][[facetvar]]=names(df1)[[i]]
}
df2<-map_df(df1,rbind)
df3<-df2 %>%complete(!!mapping$fill,fill=list(n=0,ratio=0,label=""))
df3<-data.frame(df3)
df3
}
df2
}
xlabels = levels(factor(df2[[1]]))
xlabels
ylabels = levels(factor(data[[fillvar]]))
ylabels
if (contmode) {
total=nrow(data)
ycount = length(ylabels)
(pos = 1:ycount)
y = (100/ycount) * (pos - 1) + (100/ycount)/2
if(facetbycol==FALSE) y=y*(total/100)
} else {
if(ylabelMean){
y=rowMeans(matrix(df2$y,nrow=length(ylabels)))
} else{
df2
if(is.null(facetvar)){
y=df2$y[df2$xno==1]
y[which(df2$ratio[df2$xno==1]==0)]=NA
yend=df2$y[df2$xno==max(df2$xno)]
yend[which(df2$ratio[df2$xno==max(df2$xno)]==0)]=NA
if(xreverse){
ytemp=y
y=yend
yend=ytemp
}
if(any(is.na(y))) sec.y.axis=TRUE
} else{
condition=(df2$xno==1)&(df2[[facetvar]]==unique(df2[[facetvar]])[1])
y=df2$y[condition]
y[which(df2$ratio[condition]==0)]=NA
condition1=(df2$xno==max(df2$xno))&
(df2[[facetvar]]==unique(df2[[facetvar]])[length(unique(df2[[facetvar]]))])
yend=df2$y[condition1]
yend[which(df2$ratio[condition1]==0)]=NA
if(xreverse){
ytemp=y
y=yend
yend=ytemp
}
if(any(is.na(y))) sec.y.axis=TRUE
}
}
}
if(!is.null(facetvar)){
if(facetbycol==FALSE) hide.legend=FALSE
}
if (is.numeric(df2[[fillvar]]))
df2[[fillvar]] = factor(df2[[fillvar]])
df2
p <- ggplot(mapping = aes_string(xmin = "xmin", xmax = "xmax",
ymin = "ymin", ymax = "ymax", fill = fillvar), data = df2)
p <- p +geom_rect_interactive(aes_string(tooltip = "tooltip",
data_id = "data_id"), size = size, colour = colour,...)
# p <- p +geom_rect_interactive(aes_string(tooltip = "tooltip",
# data_id = "data_id"), size = size, colour = colour)
# p
if(!is.null(facetvar)) {
addNumber<-function(string){
if ((stat == "identity") & (!is.null(yvar))){
result=sapply(string,function(x){paste0(facetvar,":",x,"\nN=",
sum(data[data[[facetvar]]==x,"n"]) )})
} else{
result=sapply(string,function(x){paste0(facetvar,":",x,"\nN=",nrow(data[data[[facetvar]]==x,]))})
}
result
}
if(is.null(labeller)){
if(facetbycol){
p<-p+eval(parse(text=paste0("facet_grid(.~",facetvar,",scales='free_x',space='free',labeller=labeller(.default=addNumber))")))
} else{
p<-p+eval(parse(text=paste0("facet_grid(",facetvar,"~.,scales='free_y',space='free_y',switch='y',labeller=labeller(.default=addNumber))")))
}
} else{
if(facetbycol){
p<-p+eval(parse(text=paste0("facet_grid(.~",facetvar,",scales='free_x',space='free',labeller=",labeller,")")))
} else{
p<-p+eval(parse(text=paste0("facet_grid(",facetvar,"~.,scales='free_y',space='free_y',switch='y',labeller=",labeller,")")))
}
}
}
p
# x=rowMeans(matrix(unique(df2$x),nrow=length(xlabels)))
# if (contmode) {
# p <- p + scale_x_continuous(breaks = xmax, labels = xlabels,name=xlab,
# limits = c(0, total))
# }else {
# #if(length(x)!=length(xlabels)) xlabels=c(xlabels,NA)
# p<-p + scale_x_continuous(breaks = NULL, labels = NULL, name=xlab)
# }
if(!is.null(facetvar)) p<-p + scale_x_continuous(breaks = NULL, labels = NULL, name=xlab)
direction = ifelse(reverse, -1, 1)
if ((position != "dodge") & hide.legend ){
if(sec.y.axis){
if(yreverse){
p <- p + scale_y_reverse(breaks = y, labels = ylabels,name=filllab,
sec.axis=sec_axis(trans=~.,breaks = yend, labels = ylabels,name=filllab))
} else{
p <- p + scale_y_continuous(breaks = y, labels = ylabels,name=filllab,
sec.axis=sec_axis(trans=~.,breaks = yend, labels = ylabels,name=filllab))
}
} else{
if(yreverse){
p<-p + scale_y_reverse(breaks = y, labels = ylabels,name=filllab)
} else{
p<-p + scale_y_continuous(breaks = y, labels = ylabels,name=filllab)
}
}
p<- p+ scale_fill_brewer(palette = palette, direction = direction,
guide = FALSE) + ylab("")
} else{
p <- p + ylab("count")+guides(fill=guide_legend(reverse=TRUE))
p <- p + scale_fill_brewer(palette = palette,
direction = direction)
}
p
if (addlabel)
p = p + geom_text(aes_string(x = "x", y = "y", label = "label"),size=labelsize)
if(is.null(xangle)){
if(max(nchar(colnames(df2)))>10) xangle=20
else xangle=0
}
p<-p+theme(axis.text.x=element_text(angle=xangle,vjust = 0.5))
p
if(is.null(yangle)) yangle=90
p <- p + theme(axis.text.y = element_text(angle = yangle),
axis.text.y.right = element_text(angle = -yangle),
axis.ticks.y = element_blank())
df3=df2[df2$yno==1,]
vjust=ifelse(facetbycol,1.8,1)
if(yreverse) vjust=ifelse(facetbycol,-1,-0.1)
if(contmode){
total=nrow(data)
df3
df3$ratio1=df3$width/total
df3$label=stringr::str_extract(substr(df3[[xvar]],2,nchar(df3[[xvar]])),"^[^,]+")
if(mean(as.numeric(df3$label))>1e+9) {
df3$label=paste0(as.numeric(df3$label)/1e+9,"T")
} else if(mean(as.numeric(df3$label))>1e+6) {
df3$label=paste0(as.numeric(df3$label)/1e+6,"M")
} else if(mean(as.numeric(df3$label))>1e+3) {
df3$label=paste0(as.numeric(df3$label)/1e+3,"K")
}
df3$ratio2=lag(df3$ratio1)
df3$ratio2[1]=df3$ratio1[1]
df3$label[(df3$ratio1<minlabelgroup)&(df3$ratio2<minlabelgroup)]=""
p
if(is.null(facetvar)){
if(xreverse){
p<-p + scale_x_reverse(breaks = df3$xmin,labels = df3$label,name=xlab)
} else{
p<-p + scale_x_continuous(breaks = df3$xmin,labels = df3$label,name=xlab)
}
} else{
p<-p + geom_text(aes_string(x = "xmin", y = "0", label = "label"),data=df3,vjust=vjust)
}
} else{
if(is.null(facetvar)){
if(xreverse){
p<-p + scale_x_reverse(breaks = df3$x,labels = df3[[xvar]],name=xlab)
} else{
p<-p + scale_x_continuous(breaks = df3$x,labels = df3[[xvar]],name=xlab)
}
} else{
if(!is.factor(df3[[xvar]])) df3[[xvar]]=factor(df3[[xvar]])
df3$label2=ifelse(df3$ratio>=0,levels(df3[[xvar]]),"")
if(is.null(family)){
p<-p + geom_text(aes_string(x = "x", y = ifelse(yreverse,"100","0"), label = "label2"),
data=df3,vjust=vjust)
} else{
p<-p + geom_text(aes_string(x = "x", y = ifelse(yreverse,"100","0"), label = "label2"),
data=df3,vjust=vjust,family=family)
}
}
}
if(!is.null(family)) p<-p+theme(text= element_text(family=family))
if(facetbycol==FALSE){
if(yreverse){
p<-p + scale_y_reverse(breaks = NULL, labels = NULL,name=NULL)
} else{
p<-p + scale_y_continuous(breaks = NULL, labels = NULL,name=NULL)
}
p <- p + theme(legend.position="bottom")
}
p
if(!is.null(facetvar)) p<-p+theme(strip.placement = "outside")
if (polar == TRUE)
p <- p + coord_polar()
if (interactive){
tooltip_css <- "background-color:white;font-style:italic;padding:10px;border-radius:10px 20px 10px 20px;"
hover_css = "fill-opacity=.3;cursor:pointer;stroke:gold;"
p<-girafe(ggobj=p)
p<-girafe_options(p,
opts_hover(css=hover_css),
opts_tooltip(css=tooltip_css,opacity=.75),
opts_zoom(min=1,max=10))
}
p
}
num2cutData=function(data,xvar,fillvar,width=0.9,position="fill",digits=1,facetbycol=TRUE,
minlabelgroup=0.04,minlabel=2){
result = num2cut(data[[xvar]])
result
b = result$x1
breaks = result$breaks
a = table(data[[fillvar]], b)
a
df=as.data.frame(a,stringsAsFactors = FALSE)
# df = reshape2::melt(a)
df = df[c(2, 1, 3)]
colnames(df) = c(xvar, fillvar, "n")
df
a
my_sumSub(df,a,width=width,position=position,digits=digits,facetbycol=facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
}
my_sumSub=function(df,a,width=0.9,position="fill",digits=1,facetbycol=TRUE,minlabelgroup=0.04,minlabel=2){
# acs$Dx=factor(acs$Dx,levels=c("Unstable Angina","NSTEMI","STEMI"))
# df=acs %>% group_by(Dx,smoking) %>%summarize(n=n())
# a=table(acs$smoking,acs$Dx)
# width=0.9;position="fill";digits=1;facetbycol=TRUE;
# minlabelgroup=0.04,minlabel=2
#
# str(df)
# str(a)
(total = sum(a))
(csum = colSums(a))
(rsum = rowSums(a))
(xmax = cumsum(csum))
(xmin = cumsum(csum) - csum)
(x = (xmax + xmin)/2)
(width = csum * width)
(xmax = x + width/2)
(xmin = x - width/2)
df$xno=rep(1:ncol(a),each=nrow(a))
df$yno=rep(1:nrow(a),ncol(a))
df=as.data.frame(df)
df
df$csum = rep(csum,each=nrow(a))
df$xmin = rep(xmin,each=nrow(a))
df$xmax = rep(xmax,each=nrow(a))
df$x = rep(x,each=nrow(a))
df$width = rep(width,each=nrow(a))
count = max(df$xno,na.rm=TRUE)
df
count
if (position == "dodge") {
df$ymax = df$n
df$ymin = 0
df
df$y = (df$ymax + df$ymin)/2
ycount = max(df$yno,na.rm=TRUE)
df$xmin2 = df$xmin + (df$yno - 1) * (df$width/ycount)
df$xmax2 = df$xmin2 + (df$width/ycount)
df$xmin = df$xmin2
df$xmax = df$xmax2
df$x = (df$xmax + df$xmin)/2
df2 = df
} else {
for (i in 1:count) {
dfsub = df[df$xno == i, ]
dfsub$ratio = round(dfsub$n * 100/csum[i], digits)
dfsub$ymax = cumsum(dfsub$n)
dfsub$ymin = dfsub$ymax - dfsub$n
if (position == "fill") {
dfsub$ymax = dfsub$ymax * 100/csum[i]
dfsub$ymin = dfsub$ymin * 100/csum[i]
}
dfsub$y = (dfsub$ymin + dfsub$ymax)/2
if (i == 1) {
df2 = dfsub
} else {
df2 = rbind(df2, dfsub)
}
df2
}
}
df2$data_id = as.character(1:nrow(df2))
df2$tooltip = paste0(df2[[2]], "<br>", df2[[1]],
"<br>", df2$nrow)
df2$label = ifelse((df2$csum/total) >= minlabelgroup, df2$n, "")
df2$tooltip = paste0(df2$tooltip, "(", df2$ratio, "%)")
if (position == "fill") {
df2$label = ifelse((df2$csum/total) >= minlabelgroup,
ifelse(df2$ratio >= minlabel,percent(df2$ratio/100),""),"")
}
df2
if(facetbycol==FALSE){
df2$xmin=df2$xmin/total
df2$xmax=df2$xmax/total
df2$x=df2$x/total
df2$ymin=df2$ymin*(total/100)
df2$ymax=df2$ymax*(total/100)
df2$y=df2$y*(total/100)
}
df2
}
my_summarize_n=function(data,mapping,width=0.9,position="fill",digits=1,facetbycol=TRUE,
minlabelgroup=0.04,minlabel=2){
# data=mtcars;mapping=aes(x=carb,fill=gear)
# width=0.9;position="fill";digits=1;facetbycol=TRUE
# minlabelgroup=0.04;minlabel=2
#
# data[[mapping$fill]]=factor(data[[mapping$fill]])
#
# df<-data %>%
# group_by( !!mapping$x,!!mapping$fill) %>%
# dplyr::summarize(n=n()) %>%
# tidyr::complete(!!mapping$fill,fill=list(n=0))
# df=data.frame(df)
# df
xvar=getMapping(mapping,"x")
fillvar=getMapping(mapping,"fill")
a=table(data[[xvar]],data[[fillvar]])
df=data.frame(a)
colnames(df)=c(xvar,fillvar,"n")
df<-df %>% arrange(!!mapping$x,!!mapping$fill)
my_sumSub(df,t(a),width=width,position=position,digits=digits,facetbycol=facetbycol,
minlabelgroup=minlabelgroup,minlabel=minlabel)
}
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