how to add row labels (annotations) in Heatmap

Question

I have the following script for creating a heatmap using Heatmap in Rstudio. Everything looks good, the coloring, dendogram size and location, font size, column annotations (labels), but I can't seem to add row labels.

My data file is tab separated text file, with a header row (column names in Heatmap), and the 1st column has the sample names (I want those to show as row labels in Heatmap)

Here is my script:

source("https://bioconductor.org/biocLite.R")
biocLite("ComplexHeatmap")
library(ComplexHeatmap)
filename <- "Data.txt"

my_data <- read.table(filename, sep ="\t", quote = "", stringsAsFactors =`FALSE,header = TRUE)`

# Make the heatmap data into a matrix
# [all rows, columns 2-13]
# Leave out 1st column (sample names) since they don't not belong in the heatmap

my_matrix <- as.matrix(my_data[ ,c(2:13)]) 

# Cluster by rows only, not columns
# Increase dendogram width
# Change font size to 0.8

Heatmap(my_matrix, cluster_columns = FALSE, 
        column_names_gp = gpar(cex=0.8),
        row_hclust_width = unit(3, "cm"))

Everything looks great, but there are no row labels on my heatmap (only column labels).

Answer 1

Sorry this is a little late but can you switch the row names on your matrix:

rownames(my_matrix) <- my_matrix[,1]

Then introduce the show_row_names argument:

Heatmap(my_matrix, cluster_columns = FALSE, 
                column_names_gp = gpar(cex=0.8),
                row_hclust_width = unit(3, "cm")
                show_row_names = TRUE)

Or alternatively you can add row labels as an annotation:

ht  <- Heatmap(my_matrix, cluster_columns = FALSE, 
                column_names_gp = gpar(cex=0.8),  
                row_hclust_width = unit(3, "cm"))

ha_row <- rowAnnotation(names = row_anno_text(x = paste( my_matrix[,1]), just = "left", gp = gpar(fontsize = 11) ), show_annotation_name = FALSE)

draw(ht + ha_row)