I have been trying to add row annotation in my heatmap created by pheatmap in R. Basically I have a csv file with one particular column (Group) to be used for row annotation in heatmap. However, I'm having trouble with my following codes. The other two issues are: the font size of the title is apparently too big but I could not find a way to decrease it. And I wanted to set the values of any zero to color purewhite but I am not sure it is really white in my output file. The input csv file and the output pdf file are linked. I am sticking with pheatmap here since I found that it creates the heatmap that fits my need better than other heatmap functions. Suggestions are appreciated.
library("pheatmap")
data <- read.csv("/Users/neo/Test_BP_052215.csv", header = TRUE, row.names = 2, stringsAsFactors=F)
head(data)
Group WT KO1 KO2
GO:0018904 organic ether metabolic process Metabolism 12.17372951 0.000000 -15.006995
GO:0006641 triglyceride metabolic process Metabolism 5.200847907 0.000000 0.000000
GO:0045444 fat cell differentiation Metabolism 6.374521098 0.000000 -7.927192
GO:0006639 acylglycerol metabolic process Metabolism 6.028616852 0.000000 0.000000
GO:0016125 sterol metabolic process Metabolism 5.760678325 8.262778 0.000000
GO:0016126 sterol biosynthetic process Metabolism -6.237114754 9.622373 0.000000
heatdata <- data[,-1]
head(heatdata)
WT KO1 KO2
GO:0018904 organic ether metabolic process 12.17372951 0.000000 -15.006995
GO:0006641 triglyceride metabolic process 5.200847907 0.000000 0.000000
GO:0045444 fat cell differentiation 6.374521098 0.000000 -7.927192
GO:0006639 acylglycerol metabolic process 6.028616852 0.000000 0.000000
GO:0016125 sterol metabolic process 5.760678325 8.262778 0.000000
GO:0016126 sterol biosynthetic process -6.237114754 9.622373 0.000000
annotation_row <- data.frame(Group = data[,1])
rownames(annotation_row) = paste("Group", 1:38, sep = "")
ann_colors = list( Group = c(Metabolism="navy", Cellular="skyblue", Signal="steelblue", Transport="green", Cell="purple", Protein="yellow", Other="firebrick") )
head(annotation_row)
Group
Group1 Metabolism
Group2 Metabolism
Group3 Metabolism
Group4 Metabolism
Group5 Metabolism
Group6 Metabolism
col_breaks = unique(c(seq(-16,-0.5,length=200), seq(-0.5,0.5,length=200), seq(0.5,20,length=200)))
my_palette <- colorRampPalette(c("blue", "white", "red"))(n = 599)
pheatmap(heatdata, main="Enrichment", color=my_palette, breaks=col_breaks, border_color = "grey20", cellwidth = 15, cellheight = 12, scale = "none", annotation_row = annotation_row, annotation_colors = ann_colors, cluster_rows = F, cluster_cols=F, fontsize_row=10, filename="heatmap_BP_test.pdf")