[BioC] heatmap.2: Colv dendrogram doesn't match size of x

[Sean Davis]

On Wed, Aug 27, 2014 at 7:06 PM, <ferreirafm at usp.br> wrote:

> Hi List,
> I've got some problems doing a heatmap with following peace of code:
>
> library(gplots)
> row_distance = dist(dfdat_zscore, method =manhattan")
> row_cluster = hclust(row_distance, method = "ward.D")
> col_distance = dist(dfdat_zscore, method = "manhattan")
> col_cluster = hclust(col_distance, method = "ward.D")
>

Assuming that dfdat_zscore is not a square matrix, row_distance should be
using the transpose of that matrix.  As it stands, you are calculating the
distance between the columns for both col_distance and row_distance.  Make
that adjustment and see if that fixes your problem.

Sean



>
> heatmap.2(as.matrix(dfdat_zscore),
> main = "Z-score",
> notecol="black",
> density.info="none",
> trace="none",
> margins =c(12,9),
> col=redgreen(75),
> breaks=col_breaks,
> dendrogram = "both",
> cexCol=0.5, cexRow=0.5,
> key=T, keysize=1.0,
> Rowv = as.dendrogram(row_cluster),
> Colv = as.dendrogram(col_cluster),
> distfun = dist(method = "manhattan"),
> hclustfun = hclust(col_distance, method = "ward.D"),
> labRow=rownames(df_zscore))
>
> I've read some posts suggesting to upgrade gplots. However, the issue
> seems to persist with gplots_2.14.1
> Any help is appreciated.
> Best.
>
> Additional information:
> > sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] gplots_2.14.1
>
> loaded via a namespace (and not attached):
> [1] KernSmooth_2.23-12 bitops_1.0-6 caTools_1.17 gdata_2.13.3
> [5] gtools_3.4.1
>
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