Color key and histogram in biclustering by DESEQ2
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3.2 years ago
learner • 0

Can anyone explain me color key and Histogram on the right top? what does values and count in axis correspond to? I used DESEQ2.

hmcol <- colorRampPalette(brewer.pal(9, "GnBu"))(100)
distsRL <- dist(t(assay(rld)))
mat <- as.matrix(distsRL)
rownames(mat) <- colnames(mat)
hc <- hclust(distsRL)
heatmap.2(mat, Rowv=as.dendrogram(hc),symm=TRUE, trace="none",col = rev(hmcol), margin=c(17, 17))


https://imgur.com/0FM073P

RNA-Seq DESEQ2 clustering • 1.7k views
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thanks Kevin for nice explanation.

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Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

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3.2 years ago

It's a histogram illustrating the frequency of the Euclidean distances between your samples. The lowest Euclidean distances (closely related samples) are shaded dark blue, whilst the highest Euclidean distances (distantly related samples) are shaded a very pale green.

The peaks in the histogram just indicate where most Euclidean distances lie, ie:

• Euclidean distance 0 (frequency of 8 due to 8 samples, each being Euclidean distance of 0 when compared to itself)
• Euclidean distance 18-22
• Euclidean distance ~80

You can change the labelling of the key to reflect this with key.xlab="Euclidean distance" and key.ylab="Frequency" Kevin