Emmanuel Paradis, the maintainer of the ape package was very helpful
in solving this problem. It seems that it heatmap does not reorder
the rows, so you must reorder them or change the heatmap code to do
so. The heatmap maintainers will document this, but not change the
behavior. The following
Jim Lemon wrote:
Xiaohui wrote:
... Then, I did a heatmap for 'test' matrix. But for now, I want to
specify each of the cell in the heatmap according to the values of
the corresponding matrix elements of test.
Let's say: col-c(red,yellow,green)
for test[1,1], the color on the map should
Xiaohui wrote:
...
Then, I did a heatmap for 'test' matrix. But for now, I want to specify
each of the cell in the heatmap according to the values of the
corresponding matrix elements of test.
Let's say: col-c(red,yellow,green)
for test[1,1], the color on the map should be red.
I
You can use
plot(y~x,col=color.index.in.palette.defined.from(z),pch=20,type=p)
where
color.index.in.palette.defined.from(z)
is a function or an expression, returning either a color index in a
predefined palette or any other color representation, suitable for R. This
is described in ?par.
I
On 12/22/06, Yuli Zhou [EMAIL PROTECTED] wrote:
Hi,
How do I anchor z=0 to the white color in a levelplot so that
the color changes from cyan to magenta precisely as
z changes from negative to positive?
The changepoints are defined by 'at', and the colors are chosen more
or less linearly, so
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:
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,
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
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
You can change the code of layout:
layout(lmat, widths = lwid, heights = lhei, respect = TRUE)
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
(best to create a new function my.layout with the modified code)
Jacob Michaelson wrote:
Hi all,
Does anyone know of a fairly easy way
Andrea Zangrando wrote:
Hi,
i created a graph with heatmap(sma) function:
heatmap(dataHeat(x))
and I wish to change the gradation of colors from blue to red, how could
i do?
Using heatmap(dataHeat(x), col=c(2,4)) i will use only 2 colors
without gradation.
The color.gradient
On Tue, 4 Oct 2005, Jim Lemon wrote:
Andrea Zangrando wrote:
Hi,
i created a graph with heatmap(sma) function:
heatmap(dataHeat(x))
and I wish to change the gradation of colors from blue to red, how could
i do?
Using heatmap(dataHeat(x), col=c(2,4)) i will use only 2
Andrea == Andrea Zangrando [EMAIL PROTECTED]
on Tue, 04 Oct 2005 15:00:27 +0200 writes:
Andrea Hi,
Andrea another problem on heatmaps... after generating the graph with
Andrea myBlRd - colorRampPalette(c(blue, red))
Andrea heatmap(dataHeat[Top100, ], col=myBlRd(15))
Le 03.10.2005 14:24, Andrea Zangrando a écrit :
Hi,
i created a graph with heatmap(sma) function:
heatmap(dataHeat(x))
and I wish to change the gradation of colors from blue to red, how could
i do?
Using heatmap(dataHeat(x), col=c(2,4)) i will use only 2 colors
without gradation.
Ty so much
Andrea Zangrando a écrit :
... and I wish to change the gradation of colors
from blue to red, how could i do?
Hello,
here's how I build such a palette.
a = 15;
palwhiteblue = rgb(a:0, a:0, a, max=a);
palredwhite = rgb(a, 0:a, 0:a, max=a);
palwhite = rep(rgb(1,1,1), 8);
palRWB =
On Mon, 3 Oct 2005, Romain Francois wrote:
Le 03.10.2005 14:24, Andrea Zangrando a écrit :
Hi,
i created a graph with heatmap(sma) function:
heatmap(dataHeat(x))
and I wish to change the gradation of colors from blue to red, how could
i do?
Using heatmap(dataHeat(x), col=c(2,4)) i
Does any other plotting function work as they should e.g. plot(1:10) or
are you connecting remotely to a server ?
Regards, Adai
On Mon, 2005-09-12 at 10:51 -0400, Peter Scacheri wrote:
I'm having trouble with the heatmap function in R. When I try and
heatmap something, my graphics window
Peter Scacheri a écrit :
I'm having trouble with the heatmap function in R. When I try and
heatmap something, my graphics window does not open. Does anyone
know if this is a glitch in the version of R that I'm using? I've
listed my version of R below, as well as a simple heatmap
Hmmm...Seems to work OK now. Thanks for your help.
Peter
At 11:30 AM -0400 9/12/05, [EMAIL PROTECTED] wrote:
Peter Scacheri a écrit :
I'm having trouble with the heatmap function in R. When I try and
heatmap something, my graphics window does not open. Does anyone
know if this is a
On 8/8/05 9:45 AM, Jacob Michaelson [EMAIL PROTECTED] wrote:
Hi all,
In heatmap's documentation, it mentions that the output value is
actually an invisible list...how would one access this list?
Mylist - heatmap()
__
R-help@stat.math.ethz.ch
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
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 --
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
-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
From: Charles Plessy
Dear list,
I hope it is not a FAQ, but I searched the archives and Google, and
found nothing. The question is simple :
I do not understand why, starting from a symmetrical
correlation matrix,
heatmap produces an asymmetrical image.
Umm... because you haven't
On Jun 16, 2005, at 9:47 AM, Jacob Michaelson wrote:
Hi all,
Does anyone know of a fairly easy way to stretch a heatmap
vertically? I've got 42 arrays and would like to be able to see as
many significant genes as possible (right now I can only get 50 genes
with it still being readable).
Hello,
I was just doing heatmaps myself ;-) and I had the same problem. It would be
nice to have such an example in the help file because it is not clear (thank
you).
you use (for example... this is my case, which I am doing the distance
matrix using vegdist function with Bray curtis
:22 AM
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Subject: Re: [R] heatmap help
Hello,
I was just doing heatmaps myself ;-) and I had the same problem.
It would be
nice to have such an example in the help file because it is not
clear (thank
you).
you use (for example... this is my
I believe you want to pass the (symmetric) matrix as is, rather than wrapped
in as.dist(). E.g.,
x - as.matrix(dist(matrix(rnorm(100), 20, 5)))
heatmap(x, symm=TRUE, scale=none)
HTH,
Andy
From: Paul Lepp
Dear R wizards,
Hopeful someone can help me with what I believe is a
pretty
Sorry. I think you need the argument distfun=as.dist. E.g.,
heatmap(x, distfun=as.dist, symm=TRUE, scale=none)
Andy
From: Liaw, Andy
I believe you want to pass the (symmetric) matrix as is,
rather than wrapped
in as.dist(). E.g.,
x - as.matrix(dist(matrix(rnorm(100), 20, 5)))
Look into ?cutree.
Sean
On 5/5/04 1:29 PM, Hyung Cho [EMAIL PROTECTED] wrote:
I am using heatmap to cluster genes in microarrays. It works fine with
100~200 genes.
But when I draw a heatmap with 600 genes, I can't read a clustering tree
well.
Maybe I will be able to read it by dividing
AndyL == Liaw, Andy [EMAIL PROTECTED]
on Fri, 17 Oct 2003 09:10:16 -0400 writes:
AndyL One of the good thing about R (and S in general, I
AndyL guess) is that if a function does mostly what you
AndyL want, except for some small things, you can just make
AndyL another copy of
On Wed, Sep 24, 2003 at 02:47:21PM +0200, Martin Olivier wrote:
Hi all,
The function heatmap uses the functions dist and hclust with default
parameters.
How to change these parameters? For example, i want to use the ward
criterion for hierarchical
clustering with binary distance.
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