CODEWITHSUNDEEP
r
Lee
Lee

Reputation: 25

Setting color key to a numerical range

I generated heatmap using heatmap.2 function in R and tried to make two modifications

  1. The colour key scale need to range 5,10,15. However, I could not set that range for the scale by changing the following line, 

    colors = c(seq(0,5,length=100), seq(5,10,length=100), seq(10,15,length=100))

  2. Number (like 1, 2 3 upto the total number of rows) is shown to the end of each row and I could not delete it.

So, I look forward any suggestion to set the scale and remove the numbered Y-axis.

library(gplots)
library(RColorBrewer)
dat <- read.csv("C:/Users/anikng/Desktop/stress.csv")
dat_matrix <- data.matrix(dat)
colors = c(seq(0,5,length=100),seq(5,10,length=100),seq(10,15,length=100))
my_palette <- colorRampPalette(c("green","black","red"))(n = 299)
heatmap.2(dat_matrix, dendrogram="none", Rowv=FALSE, Colv=FALSE, col = my_palette,     breaks=colors, scale="none", key=TRUE, density.info="none", trace="none", symm=F,symkey=T,symbreaks=T)

Upvotes: 0

Views: 382

Answers (1)

csgillespie
csgillespie

Reputation: 60462

When asking a question it's always easier if you can provide some example data, so

library(gplots)
library(RColorBrewer)
dat_matrix= matrix(rnorm(1000, 10, 3), ncol=10)

  1. The issue with the range in the symkey was caused by the symkey=TRUE argument. Removing that argument, your code now works

    breaks = c(seq(min(dat_matrix), median(dat_matrix), length.out=128), 
   seq(median(dat_matrix), max(dat_matrix), length.out=128))

heatmap.2(dat_matrix, dendrogram="none", Rowv=FALSE, Colv=FALSE, breaks=breaks, 
         key=TRUE, density.info="none", trace="none", col=my_palette)

  2. To remove the numbers from the graph, add the arguments: labRow=FALSE and labCol=FALSE

Upvotes: 1

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