Re: [R] heatmap color distribution
You can use the breaks argument in image to do this. (You don't specify a function you're using, but other heatmap functions probably have a similar parameter.) Look across all your data, figure out the ranges you want to have different colors, and specify the appropriate break points in each call to image. Then you're using the same color set in each one. You run the risk, of course, that some of your images will have a very narrow color range, which might obscure interesting features. But nothing stops you from making more than one plot. Hope this helps. Regards, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Michaelson Sent: Thursday, July 21, 2005 9:26 AM To: r-help@stat.math.ethz.ch Subject: [R] heatmap color distribution Hi all, I've got a set of gene expression data, and I'm plotting several heatmaps for subsets of the whole set. I'd like the heatmaps to have the same color distribution, so that comparisons may be made (roughly) across heatmaps; this would require that the color distribution and distance functions be based on the entire dataset, rather than on individual subsets. Does anyone know how to do this? Thanks in advance, Jake __ 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 __ 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 color distribution
Thanks for the reply. As I understand it, breaks only controls the
binning. The problem I'm having is that each subset heatmap has
slightly different min and max log2 intensities. I'd like the colors
to be based on the overall (complete set) max and min, not the subsets'
max and min -- I could be wrong, but I don't think breaks will help
me there. And you're right - this might obscure some of the
trends/features, but we'll also plot the default heatmaps.
Also (I should have specified) I'm using heatmap.2.
Thanks,
Jake
On Jul 21, 2005, at 8:09 AM, Wiener, Matthew wrote:
You can use the breaks argument in image to do this. (You don't
specify a
function you're using, but other heatmap functions probably have a
similar
parameter.) Look across all your data, figure out the ranges you want
to
have different colors, and specify the appropriate break points in
each call
to image. Then you're using the same color set in each one. You run
the
risk, of course, that some of your images will have a very narrow color
range, which might obscure interesting features. But nothing stops
you from
making more than one plot.
Hope this helps.
Regards,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jacob Michaelson
Sent: Thursday, July 21, 2005 9:26 AM
To: r-help@stat.math.ethz.ch
Subject: [R] heatmap color distribution
Hi all,
I've got a set of gene expression data, and I'm plotting several
heatmaps for subsets of the whole set. I'd like the heatmaps to have
the same color distribution, so that comparisons may be made
(roughly) across heatmaps; this would require that the color
distribution and distance functions be based on the entire dataset,
rather than on individual subsets. Does anyone know how to do this?
Thanks in advance,
Jake
__
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http://www.R-project.org/posting-guide.html
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Re: [R] heatmap color distribution
Breaks affects the binning into colors. Try this. Assume that temp is one
of your data sets. It's values are restricted to 0.25 - 0.75, and we'll
assume that the full data set goes from 0 to 1.
temp - matrix(runif(60, 0.25, 0.75), nc = 6)
breaks - seq(from = 0, to = 1, length = 11)
image(temp2, col = heat.colors(10)) # full range of
color
image(temp2, col = heat.colors(10), breaks = breaks)# muted colors
The second image is told about all the colors, and about the full range of
data through breaks, and only uses the colors in the middle.
Is that what you mean?
HTH,
Matt
-Original Message-
From: Jake Michaelson [mailto:[EMAIL PROTECTED]
Sent: Thursday, July 21, 2005 10:45 AM
To: Wiener, Matthew
Cc: R-help@stat.math.ethz.ch
Subject: Re: [R] heatmap color distribution
Thanks for the reply. As I understand it, breaks only controls the
binning. The problem I'm having is that each subset heatmap has
slightly different min and max log2 intensities. I'd like the colors
to be based on the overall (complete set) max and min, not the subsets'
max and min -- I could be wrong, but I don't think breaks will help
me there. And you're right - this might obscure some of the
trends/features, but we'll also plot the default heatmaps.
Also (I should have specified) I'm using heatmap.2.
Thanks,
Jake
On Jul 21, 2005, at 8:09 AM, Wiener, Matthew wrote:
You can use the breaks argument in image to do this. (You don't
specify a
function you're using, but other heatmap functions probably have a
similar
parameter.) Look across all your data, figure out the ranges you want
to
have different colors, and specify the appropriate break points in
each call
to image. Then you're using the same color set in each one. You run
the
risk, of course, that some of your images will have a very narrow color
range, which might obscure interesting features. But nothing stops
you from
making more than one plot.
Hope this helps.
Regards,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jacob Michaelson
Sent: Thursday, July 21, 2005 9:26 AM
To: r-help@stat.math.ethz.ch
Subject: [R] heatmap color distribution
Hi all,
I've got a set of gene expression data, and I'm plotting several
heatmaps for subsets of the whole set. I'd like the heatmaps to have
the same color distribution, so that comparisons may be made
(roughly) across heatmaps; this would require that the color
distribution and distance functions be based on the entire dataset,
rather than on individual subsets. Does anyone know how to do this?
Thanks in advance,
Jake
__
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
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Re: [R] heatmap color distribution
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Jacob Michaelson Sent: 21 July 2005 12:26 To: r-help@stat.math.ethz.ch Subject: [R] heatmap color distribution Hi all, I've got a set of gene expression data, and I'm plotting several heatmaps for subsets of the whole set. I'd like the heatmaps to have the same color distribution, so that comparisons may be made (roughly) across heatmaps; this would require that the color distribution and distance functions be based on the entire dataset, rather than on individual subsets. Does anyone know how to do this? Thanks in advance, For each heatmap, in image() set the zlim argument to c(zmin,zmax) where zmin and zmax are the minimum and maximum observed across the entire data set. Also, for each heatmap set col=heat.colors(n) to the same n for all heatmaps. I do that with image.kriging in geoR. Hope it works for you. Ruben __ 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
