Search
Question: heatmap-suppress col reordering/dendrogram?
0
gravatar for Ann Hess
12.1 years ago by
Ann Hess340
Ann Hess340 wrote:
Using the heatmap function, is there a way to suppress the column reordering and column dendrogram? I have five time points and I want to keep them in order! I have tried the following commands, but still get reordered columns: heatmap(x, Colv=FALSE... heatmap(x, Colv=NULL... Also, is there a way to suppress the row dendrogram, but still reorder the rows according to some dendrogram? I was hoping to gain space for my row labels by omitting the dendrogram. I have tried the following command, but still get the dendrogram: heatmap(x, Rowv=as.dendrogram(hc), keep.dendro=FALSE)
ADD COMMENTlink modified 12.1 years ago by Lourdes Peña Castillo140 • written 12.1 years ago by Ann Hess340
0
gravatar for Sean Davis
12.1 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On 10/26/05 11:10 AM, "Ann Hess" <hess at="" stat.colostate.edu=""> wrote: > Using the heatmap function, is there a way to suppress the column > reordering and column dendrogram? I have five time points and I want to > keep them in order! I have tried the following commands, but still get > reordered columns: > > heatmap(x, Colv=FALSE... > heatmap(x, Colv=NULL... > > Also, is there a way to suppress the row dendrogram, but still reorder the > rows according to some dendrogram? I was hoping to gain space for my row > labels by omitting the dendrogram. I have tried the following command, > but still get the dendrogram: > > heatmap(x, Rowv=as.dendrogram(hc), keep.dendro=FALSE) I like heatmap.2 from the gplots package which has a dendrogram=c('row','column','none') argument. Sean
ADD COMMENTlink written 12.1 years ago by Sean Davis21k
0
gravatar for Sean Davis
12.1 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On 10/26/05 11:18 AM, "Ann Hess" <hess at="" stat.colostate.edu=""> wrote: > Sean- > > Where do you get the gplots package? I don't see it listed with the BioC > 1.7 packages. CRAN. You can install package gregmisc which contains gplots as well as the other packages on which it depends. Sean
ADD COMMENTlink written 12.1 years ago by Sean Davis21k
0
gravatar for Lourdes Peña Castillo
12.1 years ago by
Lourdes Peña Castillo140 wrote:
Hi Ann, > Using the heatmap function, is there a way to suppress the column > reordering and column dendrogram? I have five time points and I want to > keep them in order! I have tried the following commands, but still get > reordered columns: > > heatmap(x, Colv=FALSE... > heatmap(x, Colv=NULL... Try: heatmap(x, Colv=NA,... > Also, is there a way to suppress the row dendrogram, but still reorder the > rows according to some dendrogram? I was hoping to gain space for my row > labels by omitting the dendrogram. I have tried the following command, > but still get the dendrogram: > > heatmap(x, Rowv=as.dendrogram(hc), keep.dendro=FALSE) Try using the index of the rows in your dendrogram: myDendro <- as.dendrogram(hc) rowInd <- order.dendrogram(myDendro) heatmap(x[rowInd,], Rowv=NA, ... Lourdes
ADD COMMENTlink written 12.1 years ago by Lourdes Peña Castillo140
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 255 users visited in the last hour