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") 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 [[alternative HTML version deleted]]

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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]