wrong heatmap with only two solid colors
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Entering edit mode
7.8 years ago

hi, I am making heatmap using ggplot2 after processing through the deseq and using the manual completely.

I am comparing two samples without replicates. I am struck at making the heatmap as the heatmap obtained only shows color for the genes with higher number of reads in blue color and the lower one in white when making the plot. I have tried changing the color scheme. Its not because of color scheme I guess. for e.g.

                      variety 1       variety 2
gene_id_12345
                      25000(blue)     18000(white)
gene_id_45678
                         15000(white)    19000(blue)

So instead of showing gradient colors for there two its showing variety 1 in blue color and variety 2 as white. Happening for all the genes. Therefore I am getting a binary kind of graph. I am not very good with stats but have followed the manual completely. Command :

heatmap(exprs(vsd)[select,], col = hmcol, trace="none", margin=c(10, 6))

head(vsd)
ExpressionSet (storageMode: lockedEnvironment)
assayData: 1 features, 2 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: variety1 variety2
  varLabels: sizeFactor condition
  varMetadata: labelDescription
featureData
  featureNames: AB_0001
  fvarLabels: disp_blind
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:

Instead of heatmap.2(code),my package only has heatmap(code).cuz of this?error in data?

Any help appreciated.

Thanks!!

heatmap RNA-Seq deseq ggplot2 • 2.1k views
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