R: read.table for heatplot

Question

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)

score 0 · Accepted Answer · answered Jul 10 '18 at 10:50

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))

R: read.table for heatplot

1 Answers1