Question: Add labels in the annotation bar of pheatmap
1
gravatar for xieshaojun0621
10 weeks ago by
United States
xieshaojun062190 wrote:

I have the code below to generate the heatmap with annotation. enter image description here

library(pheatmap)
# Generate some data
test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")
# Add annotation as described above, and change the name of annotation
annotation <- data.frame(Var1 = factor(1:10 %% 2 == 0, labels = c("Exp1", "Exp2")))
rownames(annotation) <- colnames(test) # check out the row names of annotation
pheatmap(test, annotation = annotation)

I'm wondering whether there is a way to add the labels in the annotation bar in R code. Thanks in advance. enter image description here

ADD COMMENTlink modified 9 weeks ago by biostart240 • written 10 weeks ago by xieshaojun062190
1

use grid.text (part of base functions, earlier part of library "grid") (play with x and y coordinates):

pheatmap(test, annotation = annotation)
grid.text(levels(annotation$Var1), x=c(0.25,0.6),y=c(0.89,0.89), gp=gpar(fontsize=10))

Rplot01

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by cpad01129.3k
0
gravatar for biostart
9 weeks ago by
biostart240
Germany
biostart240 wrote:

I think the simplest is just export as PDF and edit it in Adobe Illustrator

ADD COMMENTlink written 9 weeks ago by biostart240
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