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!!