

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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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: [hidden email]
> [mailto: [hidden email]]On Behalf Of
> Akkineni,Vasundhara
> Sent: Wednesday, February 22, 2006 12:09 PM
> To: [hidden email]
> 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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> https://stat.ethz.ch/mailman/listinfo/rhelp> PLEASE do read the posting guide!
http://www.Rproject.org/postingguide.html
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On 2/22/06 12:09 PM, "Akkineni,Vasundhara" < [hidden email]>
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
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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 10,00050,000) 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 < [hidden email]>
To: "Akkineni,Vasundhara" < [hidden email]>, rhelp < [hidden email]>
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" < [hidden email]>
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
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On 2/22/06 3:15 PM, "Akkineni,Vasundhara" < [hidden email]>
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
> 10,00050,000) 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
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