Question: Color key and histogram in biclustering by DESEQ2
0
gravatar for learner
4 months ago by
learner0
learner0 wrote:

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))

link to image :

https://imgur.com/0FM073P

clustering rna-seq deseq2 • 229 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by learner0

thanks Kevin for nice explanation.

ADD REPLYlink written 4 months ago by learner0

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

ADD REPLYlink written 4 months ago by genomax49k
0
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe21k
University College London Cancer Institute
Kevin Blighe21k wrote:

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

ADD COMMENTlink written 4 months ago by Kevin Blighe21k
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