Hello,

I am using pheatmap to map RNA-seq data. I have run into the same problem as other users, in attempting to annotate my heatmaps. Unfortunately I'm in the early stages of learning R, so I am struggling to interpret the solutions offered in other posts.

I would like to annotate my heatmap by rows (genes falling into a particular category "Genetype", as well as columns "SubcloneCohort". I get the common error message:

Error in check.length("fill") : 'gpar' element 'fill' must not be length 0

If anyone can help me understand what is amiss I'll be very grateful! Here is a link to the .CSV data file

Thanks, Oliver

The code I am using is as follows:

Read in data

data <- read.csv("DNA repair genes.csv", comment.char="#")

assign labels in column 1 to "rnames"

rnames <- data[,1]

assign labels in column 67 to "gtype"

gtype <- data[,67]

transform column 2-66 into a matrix

matrix <- data.matrix(data[,2:66])
rownames(matrix) <- rnames

Generate annotations for columns

annotation_col = data.frame( SubcloneCohort = factor(rep(c("J", "O", "P", "K", "L", "N", "Q"), c(8, 10, 9, 10, 10, 7, 11))))

rownames(annotation_col) = paste("Cohort", 1:65, sep = "")

Generate annotations for rows

annotation_row = data.frame( GeneType = factor(rep(c("Strand break joining", "Base excision repair", "Poly polymerases", "Direct reversal of damage", "Repair of topoisomerase crosslinks", "Mismatch excision repair", "Homologour recombination", "Fanconi anaemia", "Non-homologous end joining"), c(6, 11, 3, 3, 2, 9, 19, 14, 7))))

rownames(annotation_row) = paste("Gene", 1:74, sep = "")

Display column annotations

pheatmap(matrix, annotation_col = annotation_col)

Draw heatmaps

pheatmap(matrix, cluster_rows=T, cluster_cols=F, scale = "row", clustering_distance_rows = "euclidean", gaps_col = c(8, 18, 27, 37, 47, 54), border_color = FALSE, color = colorRampPalette(c("red", "black", "green"))(499), #add this for special color pallette cellwidth = 8, cellheight = 10, main = "DNA repair", fontsize = 12, fontsize_row = 8, fontsize_col = 7)