Question: wrong heatmap with only two solid colors
gravatar for shilpi.singh2811
3.9 years ago by
shilpi.singh28110 wrote:

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


                  25000(blue)     18000(white)


                     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.


heatmap rna-seq deseq ggplot2 forum • 1.2k views
ADD COMMENTlink modified 3.9 years ago by WouterDeCoster43k • written 3.9 years ago by shilpi.singh28110
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