#' A function for plotting mutiple gg plots
#'
#' Found at http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_(ggplot2)/
#'
#' ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
#'
#' @param ... ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
#' @param plotlist ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
#' @param cols Number of columns in layout
#' @param layout A matrix specifying the layout. If present, 'cols' is ignored
#' @return nothing
#'
#' @examples
#'
#' If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
# then plot 1 will go in the upper left, 2 will go in the upper right, and
# 3 will go all the way across the bottom.
multiplot = function(..., plotlist=NULL, file, cols=1, layout=NULL) {
require(grid)
require(ggplot2)
# Make a list from the ... arguments and plotlist
plots <- c(list(...), plotlist)
numPlots = length(plots)
# If layout is NULL, then use 'cols' to determine layout
if (is.null(layout)) {
# Make the panel
# ncol: Number of columns of plots
# nrow: Number of rows needed, calculated from # of cols
layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
ncol = cols, nrow = ceiling(numPlots/cols))
}
if (numPlots==1) {
print(plots[[1]])
} else {
# Set up the page
grid.newpage()
pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))
# Make each plot, in the correct location
for (i in 1:numPlots) {
# Get the i,j matrix positions of the regions that contain this subplot
matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))
print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
layout.pos.col = matchidx$col))
}
}
}
#' A function for Kaplan-Meier plots with ggplot2
#'
#' Found at https://github.com/michaelway/ggkm
#'
#'
#' @param sfit A survfit object from Survival package
#'
#' @examples
#' ggkm(survfit(Surv(RFSMonths, RFSStatus) ~ riskGroup), timeby = 12)
#'
ggkm = function(sfit,
table = TRUE,
returns = FALSE,
xlabs = "Time",
ylabs = "Survival Probability",
xlims = c(0,max(sfit$time)),
ylims = c(0,1),
ystratalabs = NULL,
ystrataname = NULL,
timeby = 100,
main = "Kaplan-Meier Plot",
pval = TRUE,
subs = NULL,
linetypes = NULL,
...) {
#############
# libraries #
#############
require(ggplot2)
require(survival)
require(gridExtra)
require(plyr)
#################################
# sorting the use of subsetting #
#################################
times <- seq(0, max(sfit$time), by = timeby)
if(is.null(subs)){
subs1 <- 1:length(levels(summary(sfit)$strata))
subs2 <- 1:length(summary(sfit,censored=T)$strata)
subs3 <- 1:length(summary(sfit,times = times,extend = TRUE)$strata)
} else{
for(i in 1:length(subs)){
if(i==1){
ssvar <- paste("(?=.*\\b=",subs[i],sep="")
}
if(i==length(subs)){
ssvar <- paste(ssvar,"\\b)(?=.*\\b=",subs[i],"\\b)",sep="")
}
if(!i %in% c(1, length(subs))){
ssvar <- paste(ssvar,"\\b)(?=.*\\b=",subs[i],sep="")
}
if(i==1 & i==length(subs)){
ssvar <- paste("(?=.*\\b=",subs[i],"\\b)",sep="")
}
}
subs1 <- which(regexpr(ssvar,levels(summary(sfit)$strata), perl=T)!=-1)
subs2 <- which(regexpr(ssvar,summary(sfit,censored=T)$strata, perl=T)!=-1)
subs3 <- which(regexpr(ssvar,summary(sfit,times = times,extend = TRUE)$strata, perl=T)!=-1)
}
if( !is.null(subs) ) pval <- FALSE
##################################
# data manipulation pre-plotting #
##################################
if(is.null(ystratalabs)) ystratalabs <- as.character(sub("group=*","",names(sfit$strata))) #[subs1]
if(is.null(ystrataname)) ystrataname <- "Strata"
m <- max(nchar(ystratalabs))
times <- seq(0, max(sfit$time), by = timeby)
.df <- data.frame( # data to be used in the survival plot
time = sfit$time[subs2],
n.risk = sfit$n.risk[subs2],
n.event = sfit$n.event[subs2],
surv = sfit$surv[subs2],
strata = factor(summary(sfit, censored = T)$strata[subs2]),
upper = sfit$upper[subs2],
lower = sfit$lower[subs2]
)
levels(.df$strata) <- ystratalabs # final changes to data for survival plot
zeros <- data.frame(time = 0, surv = 1,
strata = factor(ystratalabs, levels=levels(.df$strata)),
upper = 1, lower = 1)
.df <- rbind.fill(zeros, .df)
d <- length(levels(.df$strata))
###################################
# specifying plot parameteres etc #
###################################
p <- ggplot( .df, aes(time, surv)) +
geom_step(aes(linetype = strata), size = 0.7)
if(!is.null(linetypes)) p = p + scale_linetype_manual(values = linetypes)
p = p + theme_bw() +
theme(axis.title.x = element_text(vjust = 0.5)) +
scale_x_continuous(xlabs, breaks = times, limits = xlims) +
scale_y_continuous(ylabs, limits = ylims) +
theme(panel.grid.minor = element_blank()) +
theme(legend.position = c(ifelse(m < 10, .28, .35),ifelse(d < 4, .25, .35))) + # MOVE LEGEND HERE [first is x dim, second is y dim]
theme(legend.key = element_rect(colour = NA)) +
labs(linetype = ystrataname) +
theme(plot.margin = unit(c(0, 1, .5,ifelse(m < 10, 1.5, 2.5)),"lines")) +
ggtitle(main)
## Create a blank plot for place-holding
## .df <- data.frame()
blank.pic <- ggplot(.df, aes(time, surv)) +
geom_blank() + theme_bw() +
theme(axis.text.x = element_blank(),axis.text.y = element_blank(),
axis.title.x = element_blank(),axis.title.y = element_blank(),
axis.ticks = element_blank(),
panel.grid.major = element_blank(),panel.border = element_blank())
#####################
# p-value placement #
#####################a
if(pval) {
sdiff <- survdiff(eval(sfit$call$formula), data = eval(sfit$call$data))
pval <- pchisq(sdiff$chisq,length(sdiff$n) - 1,lower.tail = FALSE)
pvaltxt <- ifelse(pval < 0.0001,"p < 0.0001",paste("p =", signif(pval, 3)))
p <- p + annotate("text",x = 0.6 * max(sfit$time),y = 0.1,label = pvaltxt)
}
###################################################
# Create table graphic to include at-risk numbers #
###################################################
if(table) {
risk.data <- data.frame(
strata = factor(summary(sfit,times = times,extend = TRUE)$strata[subs3]),
time = summary(sfit,times = times,extend = TRUE)$time[subs3],
n.risk = summary(sfit,times = times,extend = TRUE)$n.risk[subs3]
)
risk.data$strata <- factor(risk.data$strata, levels=rev(levels(risk.data$strata)))
data.table <- ggplot(risk.data,aes(x = time, y = strata, label = format(n.risk, nsmall = 0))) +
#, color = strata)) +
geom_text(size = 3.5) + theme_bw() +
scale_y_discrete(breaks = as.character(levels(risk.data$strata)),
labels = rev(ystratalabs)) +
# scale_y_discrete(#format1ter = abbreviate,
# breaks = 1:3,
# labels = ystratalabs) +
scale_x_continuous("Numbers at risk", limits = xlims) +
theme(axis.title.x = element_text(size = 10, vjust = 1),
panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.border = element_blank(),axis.text.x = element_blank(),
axis.ticks = element_blank(),axis.text.y = element_text(face = "bold",hjust = 1))
data.table <- data.table +
theme(legend.position = "none") + xlab(NULL) + ylab(NULL)
data.table <- data.table +
theme(plot.margin = unit(c(-1.5, 1, 0.1, ifelse(m < 10, 2.5, 3.5) - 0.28 * m), "lines")) # ADJUST POSITION OF TABLE FOR AT RISK
#######################
# Plotting the graphs #
#######################
## p <- ggplotGrob(p)
## p <- addGrob(p, textGrob(x = unit(.8, "npc"), y = unit(.25, "npc"), label = pvaltxt,
## gp = gpar(fontsize = 12)))
grid.arrange(p, blank.pic, data.table, clip = FALSE, nrow = 3,
ncol = 1, heights = unit(c(2, .1, .25),c("null", "null", "null")))
if(returns) {
a <- arrangeGrob(p, blank.pic, data.table, clip = FALSE, nrow = 3,
ncol = 1, heights = unit(c(2, .1, .25), c("null", "null", "null")))
return(a)
}
} else {
## p <- ggplotGrob(p)
## p <- addGrob(p, textGrob(x = unit(0.5, "npc"), y = unit(0.23, "npc"),
## label = pvaltxt, gp = gpar(fontsize = 12)))
if(returns) return(p)
}
}
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