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Question: Generating heatmaps of pre-selected candidate genes after deseq2
1
gravatar for Sreeraj Thamban
3.3 years ago by
Sreeraj Thamban • 220
Indian Institute of Science Education and Research
Sreeraj Thamban • 220 wrote:

Hi biostars, Is it possible to make a heatmap for a preselected list of genes after deseq2 DGE analysis? I wanted to represent the log2FC of 20 differentially expressed candidate genes as a heatmap.
heatmap rna-seq deseq2 • 3.0k views
ADD COMMENT • link •
modified 8 weeks ago by svp • 420 • written 3.3 years ago by Sreeraj Thamban • 220

Hi, did you solve this? I want to do a similar thing with a number of candidate genes but using rlog data to include in a pheatmap

ADD REPLY • link written 9 months ago by n.tear • 20
3
gravatar for e.rempel
3.3 years ago by
e.rempel • 980
Germany, Heidelberg
e.rempel • 980 wrote:

Hi,

it is absolutely possible. Have a look at this tutorial. You could slice the matrix of normalized counts to contain only interesting genes:

pheatmap(assay(ntd)[intersting_genes,], cluster_rows=FALSE, show_rownames=FALSE,
     cluster_cols=FALSE, annotation_col=df)
ADD COMMENT • link written 3.3 years ago by e.rempel • 980

How do you "slice the matrix of normalized counts to contain only interesting genes", considering a list/data frame named "GENES_TO_LABEL" (containing the names of the genes you wish to label) which you've imported from a txt file?

ADD REPLY • link modified 19 months ago • written 19 months ago by rodd • 130

Hi, did you solve this? I want to do a similar thing with a number of candidate genes but using rlog data to include in a pheatmap

ADD REPLY • link written 9 months ago by n.tear • 20
1
gravatar for svp
8 weeks ago by
svp • 420
Bangalore
svp • 420 wrote:

You can use as follows: use a vector that contains list of genes you wish.

genes <- c("gene_1", "gene_2", ...)
mat <- assay(rld)[genes, ]
mat <- mat - rowMeans(mat)
anno <- as.data.frame(colData(rld)[c("Condition")])
pheatmap(mat, annotation_col = anno)
ADD COMMENT • link written 8 weeks ago by svp • 420
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