I have the following matrix:
row genome1 genome2 genome3
genome1 100 99.99 98.88
genome2 99.99 100 NA
genome3 98.88 NA 100
which I want to plot as a heatmap.
With the code posted below, I have problems reading the file - the rownames and header are not kept. Plus, I would like that the values are displayed with a %
on the heatmap or the NA
.
ani <-read.table(file="matrix", header=T, sep="\t", dec=".", row.names=1)
anim<-as.matrix(as.data.frame(lapply(ani, as.numeric)))
library(gplots)
my_palette <- colorRampPalette(c("red", "yellow", "green"))(n = 299)
heatmap.2(anim, notecol="black", density.info="none", trace="none", col=my_palette, cellnote=anim)
Try this:
ani <- read.table(text='
row genome1 genome2 genome3
genome1 100 99.99 98.88
genome2 99.99 100 NA
genome3 98.88 NA 100
', header=T, row.names=1, quote="")
anim <- as.matrix(ani)
library(gplots)
my_palette <- colorRampPalette(c("red", "yellow", "green"))(n = 299)
heatmap.2(anim, notecol="black", density.info="none", trace="none",
col=my_palette, cellnote=anim, margins=c(10,10))
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