Combining multiple complex plots as panels in a single figure

Question

Introduction by @backlin

Multiple simple plots can combined as panels in a single figure by using layout or par(mfrow=...). However, more

Answer 1

I struggled with a similar problem and came up with a solution that is very easy but requires imagemagick installed. The idea is to plot the heatmaps to separate files and then combine them with the montage command:

library(gplots)
row.scaled.expr <- matrix(sample(1:10000),nrow=1000,ncol=10)
arr <- array(data=row.scaled.expr, dim=c(dim(row.scaled.expr),4))
par(mfrow=c(2,2))
for (i in 1:4) {
    ifile <- paste0(i,'_heatmap.pdf')
    pdf(ifile)
    heatmap.2(arr[ , ,i], dendrogram ='row',
                        Colv=FALSE, col=greenred(800), 
                        key=FALSE, keysize=1.0, symkey=FALSE, density.info='none',
                        trace='none', colsep=1:10,
                        sepcolor='white', sepwidth=0.05,
                        scale="none",cexRow=0.2,cexCol=2,
                        labCol = colnames(arr[ , ,i]),                 
                        hclustfun=function(c){hclust(c, method='mcquitty')},
                        lmat=rbind( c(0, 3), c(2,1), c(0,4) ), lhei=c(0.25, 4, 0.25 ),                 
    )
    dev.off()
}
system('montage -geometry 100% -tile 2x2 ./*_heatmap.pdf outfile.pdf')