Example breast tumours Error in Step 4 - heatmap

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
38/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
r
Domain
data-visualization

Research direction

Reproduce the breast-tumour example through step 4 and inspect the heatmap.3 call using CNA.test, especially the RowSideColors and cells arguments. Compare their dimensions with the transposed expression matrix and confirm that the example completes with the heatmap rendered without the reported error.

Written by the indexing model from the issue text.

Description

Good afternoon,

I am currently trying to run the example with the breast tumours.
However, I get the following error in step 4 when trying to plot the heatmap.3:

` heatmap.3(t(CNA.test[,4:ncol(CNA.test)]),dendrogram="r", distfun = function(x) parallelDist::parDist(x,threads =4, method = "euclidean"), hclustfun = function(x) hclust(x, method="ward.D2"),
             ColSideColors=chr1,RowSideColors=cells,Colv=NA, Rowv=TRUE,
             notecol="black",col=my_palette,breaks=col_breaks, key=TRUE,
             keysize=1, density.info="none", trace="none",
            cexRow=0.1,cexCol=0.1,cex.main=1,cex.lab=0.1,
             symm=F,symkey=F,symbreaks=T,cex=1, cex.main=4, margins=c(10,10))


Error in heatmap.3(t(CNA.test[, 4:ncol(CNA.test)]), dendrogram = "r",  : 
  'RowSideColors' must be a matrix of ncol(x) columns`

Can you please help me with this?

Thank you!

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