Question: pheatmap: how to use legend information as row annotation?
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gravatar for n85825
12 months ago by
n858250
n858250 wrote:

I am using below code in pheatmap to generate the first heatmap.

oz <- DESeq(oz)
rld <- rlog(oz)
topVarGenes <- head(order(rowVars(assay(rld)), decreasing = TRUE), 35)
mat  <- assay(rld)[topVarGenes, ]
mat  <- mat - rowMeans(mat)
anno_col <- as.data.frame(colData(rld)[, c("time","treatment")])
anno_row <- data.frame(category = c(rep("pathway_1", 8), 
rep("CATEGORY_2", 2), rep("pathway_3", 10), 
rep("CATEGORY_4", 4), rep("limited_5", 11)), stringsAsFactors = FALSE)
mixed_name <- cbind(mat[,0],anno_row)
pheatmap(mat, annotation_col = anno_col, annotation_row = mixed_name, scale = "column", 
cluster_cols = F, cluster_rows= F, clustering_distance_rows = "correlation", 
clustering_distance_cols = "correlation", clustering_method = "average",  
gaps_row=c(8,10,20,24), 
cellheight = 6, cellwidth = 10, border_color=NA, fontsize_row = 6)

first heatmap

Now, my question is that what should be added to the above code to have the "category" legend on the left of the heatmap and close to each category color, like the second figure that I have highlighted in red.

In advance, thanks for your helps!

enter image description here

annotation pheatmap R legend • 2.4k views
ADD COMMENTlink modified 12 months ago • written 12 months ago by n858250

Have you tried annotation_name_row=T? I think the legend position is an open issue.

ADD REPLYlink written 12 months ago by Devon Ryan89k

Yes, I did. But nothing has changed.

ADD REPLYlink written 12 months ago by n858250

You may want to take a look at the ComplexHeatmap package, with which you can definitely change the position of the legends and legend text.

ADD REPLYlink written 12 months ago by Kevin Blighe41k

I think you are right! The only way is switching to ComplexHeatmap package! Thank you!

ADD REPLYlink written 12 months ago by n858250
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