Pheatmap clustering and row annotation
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Entering edit mode
@meseretbrihanu-14027
Last seen 4.0 years ago

Hi,

I have the following R code to annotate clusters by row:

My data http://dpaste.com/2DM3YAF

coldf http://dpaste.com/04D4J2X

pres <- pheatmap(tpm.filter.mean, cluster_rows=TRUE, show_rownames=FALSE, show_colnames = FALSE, cluster_cols=FALSE, annotation_col = coldf, main="Heatmap", scale="row")

pres.clust <- cbind(pres, cluster = cutree(pres$tree_row, k = 50))
pres.clust <- as.data.frame(unlist(pres.clust[,2]))
colnames(pres.clust) <- c("cluster")
ann.cols <- list(cluster=rainbow(10))

pheatmap(tpm.filter.mean, cluster_rows=TRUE, show_rownames=FALSE, show_colnames = FALSE, cluster_cols=FALSE, annotation_col=coldf, main="Heatmap", scale="row", annotation_row = pres.clust, cutree_rows = 10, annotation_colors = ann.cols)

I get the following error report.

no non-missing arguments to min; returning Infno non-missing arguments to max; returning -Inf
 Hide Traceback
Error in seq.int(rx[1L], rx[2L], length.out = nb) : 'from' must be finite

R pheatmap cutree • 7.2k views
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Entering edit mode

I tried recreating the issue and the heatmap was generated without a problem. What version of R and pheatmap are you using?

 

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