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.
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: r-help-bounces at stat.math.ethz.ch > [mailto:r-help-bounces at stat.math.ethz.ch]On Behalf Of > Akkineni,Vasundhara > Sent: Wednesday, February 22, 2006 12:09 PM > To: r-help at 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. > > ______________________________________________ > R-help at 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 ---------------------------------------------------------------------- LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
On 2/22/06 12:09 PM, "Akkineni,Vasundhara" <vasu.akkineni at louisville.edu> 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
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 <sdavis2 at mail.nih.gov> To: "Akkineni,Vasundhara" <svakki01 at netmail.louisville.edu>, r-help <r-help at 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" <vasu.akkineni at louisville.edu> 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
On 2/22/06 3:15 PM, "Akkineni,Vasundhara" <vasu.akkineni at louisville.edu> 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