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.
Question: Generating heatmaps of pre-selected candidate genes after deseq2
1
Sreeraj Thamban • 220 wrote:
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modified 8 weeks ago
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svp • 420
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3.3 years ago by
Sreeraj Thamban • 220
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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)
1
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)
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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