[R] heatmap.2 in gplots package
Hello all, I am using the heatmap.2 function in the gplots package. I want to supress the reordering of the columns of the data matrix i pass to the function. I used the statement, heatmap.2(z,Colv=FALSE,dendrogram=row,col=redgreen(75)) where z, is the matrix of data. The output i want should have the rows reordered along with the dendrogram and the columns should be in the original order without any dendrogram. For the above statement i am getting an error: Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + : dimensions of z are not length(x)(+1) times length(y)(+1) I also tried using , heatmap.2(z,Colv=NULL,dendrogram=row,col=redgreen(75)) for which i am getting the output, but the columns are reordered. How can this be done for the way in which i want the map to appear? Thanks, svakki. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] heatmap.2 in gplots package
Hello Akkineni,
This bug has already been reported and we have a tentative solution that we are
testing. I'll send you a copy of the modified code once we finish testing.
-G
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of
Akkineni,Vasundhara
Sent: Wednesday, February 22, 2006 12:09 PM
To: r-help@stat.math.ethz.ch
Subject: [R] heatmap.2 in gplots package
Hello all,
I am using the heatmap.2 function in the gplots package. I
want to supress the reordering of the columns of the data
matrix i pass to the function. I used the statement,
heatmap.2(z,Colv=FALSE,dendrogram=row,col=redgreen(75))
where z, is the matrix of data. The output i want should have
the rows reordered along with the dendrogram and the columns
should be in the original order without any dendrogram. For
the above statement i am getting an error:
Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc),
ylim = 0.5 + :
dimensions of z are not length(x)(+1) times length(y)(+1)
I also tried using ,
heatmap.2(z,Colv=NULL,dendrogram=row,col=redgreen(75))
for which i am getting the output, but the columns are
reordered. How can this be done for the way in which i want
the map to appear?
Thanks,
svakki.
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Re: [R] heatmap.2 in gplots package
On 2/22/06 12:09 PM, Akkineni,Vasundhara [EMAIL PROTECTED] wrote: Hello all, I am using the heatmap.2 function in the gplots package. I want to supress the reordering of the columns of the data matrix i pass to the function. I used the statement, heatmap.2(z,Colv=FALSE,dendrogram=row,col=redgreen(75)) where z, is the matrix of data. The output i want should have the rows reordered along with the dendrogram and the columns should be in the original order without any dendrogram. For the above statement i am getting an error: Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + : dimensions of z are not length(x)(+1) times length(y)(+1) I also tried using , heatmap.2(z,Colv=NULL,dendrogram=row,col=redgreen(75)) for which i am getting the output, but the columns are reordered. How can this be done for the way in which i want the map to appear? Use Colv=1:ncol(z), I think. Sean __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] heatmap.2 in gplots package
I used Colv=1:ncol(z), and i got the display the way i need it. Thanks. One more question, is there a way to increase the size of the color key in heatmap.2 so that all the tick values(for Eg.,in my case, values range between 10,000-50,000) can be seen clearly. In the normal case i am just able to see the initial tick value which is 10,000. Please suggest a better way to do this. Thanks for the help. svakki. -Original Message- From: Sean Davis [EMAIL PROTECTED] To: Akkineni,Vasundhara [EMAIL PROTECTED], r-help r-help@stat.math.ethz.ch Date: Wed, 22 Feb 2006 12:55:25 -0500 Subject: Re: [R] heatmap.2 in gplots package On 2/22/06 12:09 PM, Akkineni,Vasundhara [EMAIL PROTECTED] wrote: Hello all, I am using the heatmap.2 function in the gplots package. I want to supress the reordering of the columns of the data matrix i pass to the function. I used the statement, heatmap.2(z,Colv=FALSE,dendrogram=row,col=redgreen(75)) where z, is the matrix of data. The output i want should have the rows reordered along with the dendrogram and the columns should be in the original order without any dendrogram. For the above statement i am getting an error: Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + : dimensions of z are not length(x)(+1) times length(y)(+1) I also tried using , heatmap.2(z,Colv=NULL,dendrogram=row,col=redgreen(75)) for which i am getting the output, but the columns are reordered. How can this be done for the way in which i want the map to appear? Use Colv=1:ncol(z), I think. Sean __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] heatmap.2 in gplots package
On 2/22/06 3:15 PM, Akkineni,Vasundhara [EMAIL PROTECTED] wrote: I used Colv=1:ncol(z), and i got the display the way i need it. Thanks. One more question, is there a way to increase the size of the color key in heatmap.2 so that all the tick values(for Eg.,in my case, values range between 10,000-50,000) can be seen clearly. In the normal case i am just able to see the initial tick value which is 10,000. Please suggest a better way to do this. As far as I know there is not an easy way to do this without hacking the heatmap.2 code, but I could be wrong. For the purposes of making final plots, I typically find that the best thing to do is to make a PDF of the plot and then edit using Adobe or some such thing. Sean __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
