# Multiple plot function
#
# Copied from: http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_%28ggplot2%29/
#
# ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
# - cols: Number of columns in layout
# - layout: A matrix specifying the layout. If present, 'cols' is ignored.
#
# 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) {
library(grid)
# 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))
}
}
}
#' @import ggplot2
#' @export
gg.correlation <- function( samples, xcol, idcol,
geom_diag = "histogram", geom_co = "point",
colourcol = NULL )
{
pars <- unique(samples[[idcol]])
plots <- list()
for (par2 in pars)
{
for (par1 in pars)
{
# Need to call the standard stat, and pass it the geom
if (par1==par2)
{
fg <- paste0("geom_",geom_diag)
gg <- ggplot2::ggplot(data=samples[(samples[[idcol]]==par1)]) +
do.call(fg, list(ggplot2::aes_string(x=xcol,colour=colourcol)))
plots <- c(plots,list(gg))
}
else
{
fg <- paste0("geom_",geom_co)
ss <- samples[samples[[idcol]]==par1|samples[[idcol]]==par2]
cn <- colnames(ss)
cn <- cn[cn != xcol & cn != idcol]
fm <- formula( paste(paste(cn, collapse="+"), "~", idcol ))
gg <- ggplot2::ggplot(data=dcast(samples, fm)) +
do.call(fg, list(ggplot2::aes_string(x=par1,y=par2,colour=colourcol)))
plots <- c(plots,list(gg))
}
}
}
multiplot( plotlist=plots, cols = length(pars) )
return(plots)
}
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