[BioC] heatmap.2: Colv dendrogram doesn't match size of x
ferreirafm at usp.br
ferreirafm at usp.br
Thu Aug 28 20:16:58 CEST 2014
Silly me. This is it!
Thanks for helping
----- Mensagem original -----
De: "Sean Davis" <sdavis2 at mail.nih.gov>
Para: ferreirafm at usp.br
Cc: bioconductor at r-project.org
Enviadas: Quarta-feira, 27 de Agosto de 2014 20:47:46
Assunto: Re: [BioC] heatmap.2: Colv dendrogram doesn't match size of x
On Wed, Aug 27, 2014 at 7:06 PM, < ferreirafm at usp.br > wrote:
<blockquote>
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
<blockquote>
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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</blockquote>
</blockquote>
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