Generating heatmaps of pre-selected candidate genes after deseq2
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3.6 years ago

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.

RNA-Seq DESEq2 heatmap • 3.4k views
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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

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3.6 years ago
e.rempel ★ 1.0k

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)
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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?

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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

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3
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6 months ago
svp ▴ 440

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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