ggplot-heatmap.R

library(ggdendro)
library(ggplot2)
library(reshape)
library(grid)
 
## colours, generated by
## library(RColorBrewer)
## rev(brewer.pal(11,name="RdYlBu"))
my.colours <- c("#313695", "#4575B4", "#74ADD1", "#ABD9E9", "#E0F3F8", "#FFFFBF",
"#FEE090", "#FDAE61", "#F46D43", "#D73027", "#A50026")
 
mydplot <- function(ddata, row=!col, col=!row, labels=col) {
## plot a dendrogram
yrange <- range(ddata$segments$y)
yd <- yrange[2] - yrange[1]
nc <- max(nchar(as.character(ddata$labels$label)))
tangle <- if(row) { 0 } else { 90 }
tshow <- col
p <- ggplot() +
geom_segment(data=segment(ddata), aes(x=x, y=y, xend=xend, yend=yend)) +
labs(x = NULL, y = NULL) + theme_dendro()
if(row) {
p <- p +
scale_x_continuous(expand=c(0.5/length(ddata$labels$x),0)) +
coord_flip()
} else {
p <- p +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
}
return(p)
}
 
g_legend<-function(a.gplot){
## from
## http://stackoverflow.com/questions/11883844/inserting-a-table-under-the-legend-in-a-ggplot2-histogram
tmp <- ggplot_gtable(ggplot_build(a.gplot))
leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
legend <- tmp$grobs[[leg]]
return(legend)
}
##' Display a ggheatmap
##'
##' this function sets up some viewports, and tries to plot the dendrograms to line up with the heatmap
##' @param L a list with 3 named plots: col, row, centre, generated by ggheatmap
##' @param col.width,row.width number between 0 and 1, fraction of the device devoted to the column or row-wise dendrogram. If 0, don't print the dendrogram
##' @return no return value, side effect of displaying plot in current device
##' @author Chris Wallace
ggheatmap.show <- function(L, col.width=0.2, row.width=0.2) {
grid.newpage()
top.layout <- grid.layout(nrow = 2, ncol = 2,
widths = unit(c(1-row.width,row.width), "null"),
heights = unit(c(col.width,1-row.width), "null"))
pushViewport(viewport(layout=top.layout))
if(col.width>0)
print(L$col, vp=viewport(layout.pos.col=1, layout.pos.row=1))
if(row.width>0)
print(L$row, vp=viewport(layout.pos.col=2, layout.pos.row=2))
## print centre without legend
print(L$centre +
theme(axis.line=element_blank(),
axis.text.x=element_blank(),axis.text.y=element_blank(),
axis.ticks=element_blank(),
axis.title.x=element_blank(),axis.title.y=element_blank(),
legend.position="none",
panel.background=element_blank(),
panel.border=element_blank(),panel.grid.major=element_blank(),
panel.grid.minor=element_blank(),plot.background=element_blank()),
vp=viewport(layout.pos.col=1, layout.pos.row=2))
## add legend
legend <- g_legend(L$centre)
pushViewport(viewport(layout.pos.col=2, layout.pos.row=1))
grid.draw(legend)
upViewport(0)
}
##' generate a heatmap + dendrograms, ggplot2 style
##'
##' @param x data matrix
##' @param hm.colours vector of colours (optional)
##' @return
##' @author Chris Wallace
ggheatmap <- function(x,
hm.colours=my.colours) {
if(is.null(colnames(x)))
colnames(x) <- sprintf("col%s",1:ncol(x))
if(is.null(rownames(x)))
rownames(x) <- sprintf("row%s",1:nrow(x))
## plot a heatmap
## x is an expression matrix
row.hc <- hclust(dist(x), "ward")
col.hc <- hclust(dist(t(x)), "ward")
row.dendro <- dendro_data(as.dendrogram(row.hc),type="rectangle")
col.dendro <- dendro_data(as.dendrogram(col.hc),type="rectangle")
 
## dendro plots
col.plot <- mydplot(col.dendro, col=TRUE, labels=TRUE) +
scale_x_continuous(breaks = 1:ncol(x),labels=colnames(x)) +
theme(plot.margin = unit(c(0,0,0,0), "lines"))
row.plot <- mydplot(row.dendro, row=TRUE, labels=FALSE) +
theme(plot.margin = unit(rep(0, 4), "lines"))
 
## order of the dendros
col.ord <- match(col.dendro$labels$label, colnames(x))
row.ord <- match(row.dendro$labels$label, rownames(x))
xx <- x[row.ord,col.ord]
dimnames(xx) <- NULL
xx <- melt(xx)
 
centre.plot <- ggplot(xx, aes(X2,X1)) + geom_tile(aes(fill=value), colour="white") +
scale_fill_gradientn(colours = hm.colours) +
labs(x = NULL, y = NULL) +
scale_x_continuous(expand=c(0,0)) +
scale_y_continuous(expand=c(0,0),breaks = NULL) +
theme(plot.margin = unit(rep(0, 4), "lines"))
ret <- list(col=col.plot,row=row.plot,centre=centre.plot)
invisible(ret)
}
 
## test run
## simulate data
library(mvtnorm)
sigma=matrix(0,10,10)
sigma[1:4,1:4] <- 0.6
sigma[6:10,6:10] <- 0.8
diag(sigma) <- 1
X <- rmvnorm(n=100,mean=rep(0,10),sigma=sigma)
 
## make plot
p <- ggheatmap(X)
 
## display plot
ggheatmap.show(p)