Hi Steve,
That plot looks to me as though a value-to-color transformation is
performed on the logarithm of gene expression. The scale bar can be
roughly reproduced like this:
library(plotrix)
plot(0,xlim=c(0,3))
gradient.rect(0,-0.1,3,0.1,
col=color.scale(seq(0,3,0.1),
c(0.7,1,1,1,0.7,0.2),
c(0
Hello,
Just do col = rev(heat.colors(256)) ?
Hope this helps,
Rui Barradas
Às 12:55 de 21/10/19, Eleftheria Dalmaris escreveu:
Hello all,
I have made the attached heat map without a problem.
On this heat map, the yellows are my high values and the oranges are my low
values. Is there a way t
ot;Legend", xpd=TRUE)
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352
-Original Message-
From: R-help On Behalf Of Ding, Yuan Chun
Sent: Thursday, October 4, 2018 1:19 PM
To: r-help@r-project.org
Subject: Re: [R] heatmap
ot;Legend", xpd=TRUE)
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352
-Original Message-
From: R-help On Behalf Of Ding, Yuan Chun
Sent: Thursday, October 4, 2018 1:19 PM
To: r-help@r-project.org
Subject: Re: [R] heatmap.2, adding a
Hi All,
I generated the attached heatmap using the following R code and attached
testfile.
I tried to move the legend to the bottom, Can anyone help me? I have played
for 3 hours and can not resolve the problem.
I realized that in the last email, I forgot to include the "Group" variable for
Hi, you have a couple of things going on here. You can reorder your
matrix by creating an index like this:
> A_index=c(grep(".A", colnames(A)), grep(".B", colnames(A)))
and do this:
> heatmap.2(A[,A_index], dendrogram="col", Rowv = colnames(A)[A_index],
> tracecol =
NA,col=bluered(64
Thanks, Patricia! I will do it by the rows, and your explanations were
great and easy to follow!
Thank you very much for your help and time.
Andre
On Mar 4, 2017 4:18 PM, "Patricia J. Hawkins" wrote:
Hi, you have a couple of things going on here. You can reorder your
matrix by creating an ind
Hi Nils,
I don't have the GMD library, but this looks like some axis labels are
being ignored to avoid overlapping. If heatmap.3 uses base graphics
you can probably get your labels by passing empty strings to heatmap.3
and then displaying the axis with staxlab (plotrix).
Jim
On Wed, Apr 6, 2016
Pijush,
The error is a result of you having repeated color values. The warnings
can be addressed by changing the arguments that you use. Attachments are
removed from posts to R Help, so I used different data to show you an
example.
Jean
library(gplots)
data(mtcars)
x <- as.matrix(mtcars[1:6
Hi Carlos,
The error from:
readShapePoly("depto.shp")
may well be that the function cannot find the file. Assuming that
there is a file "depto.shp", is it in the working directory of R when
you issue this command? Find out by:
getwd()
I suppose that macintosh computers try to hide the actual lo
On May 22, 2015, at 10:32 AM, Carlos Javier Rincon Rodriguez wrote:
> Hi. Good morning.
>
> I am trying to load a shapefile to do a heatmap of Colombia. I using all
> this package:
>
> library(ctv)
>
> library(spatial)
>
> library(ggplot2)
>
> library(sp)
>
> library(rgdal)
>
> library(rge
Hi. Good morning.
I am trying to load a shapefile to do a heatmap of Colombia. I using all
this package:
library(ctv)
library(spatial)
library(ggplot2)
library(sp)
library(rgdal)
library(rgeos)
library(maptools)
library(ggmap)
and a using this two commands to load the file:
depto<-read
Look at the heatmap function
> John David Sorkin M.D., Ph.D.
> Professor of Medicine
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology and
> Geriatric Medicine
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Bal
I don't use these functions often enough to know their idiosyncrasies, but they
appear to treat zero like a NA, and your second file has lots of zeros. I
suspect this is due to the default way the continuous act data are 'cut"
excluding the left side of the bins. If you read the help files you m
Thank you very much for the hints. I fixed the problem.
On Thursday, December 12, 2013 2:08 PM, Kevin Wright wrote:
Read the help page for both and pay particular attention to the "scale"
argument.
Kevin Wright
On Thu, Dec 12, 2013 at 9:45 AM, capricy gao wrote:
I have a huge datas
Read the help page for both and pay particular attention to the "scale"
argument.
Kevin Wright
On Thu, Dec 12, 2013 at 9:45 AM, capricy gao wrote:
> I have a huge dataset(15k X 18) and tried to use the heatmap in R to
> examine the patterns. However, I found that heatmap and heatmap.2 gave me
You have some randomly doubled quotation marks and parentheses.
A text editor with syntax highlighting is wonderful for catching that
sort of problem.
Beyond that, see:
?heatmap
A "very urgent" request suggests homework to me, which this list doesn't do.
Though sometimes someone will offer a h
I do not want to use the b word, but can anyone who also subscribes to
the r-developer list forward my observation regarding heatmap? I am
pretty confident that the behaviour of heatmap in R 3.0.1 is not that
one intended.
On 31 July 2013 14:03, Witold E Wolski wrote:
> Would anyone of the mor
In your example all of the values are drawn from the same
distribution so there will not be substantial differences (row
means/variances and column means/variances will be
approximately the same).
set.seed(42)
d <- matrix(rnorm(100),nrow=20)
# Start with your example and modify the row/col means
On Jun 25, 2013, at 21:51 , Rui Barradas wrote:
> Hello,
>
> Your data has commas as decimal points, R uses the period. So the data is
> read in as strings, not numbers. You can change this by using argument 'dec'
> of read.table:
>
> ?read.table
> read.table(...etc..., dec = ",")
>
>
> Or
Hello,
Your data has commas as decimal points, R uses the period. So the data
is read in as strings, not numbers. You can change this by using
argument 'dec' of read.table:
?read.table
read.table(...etc..., dec = ",")
Or you can replace the commas with periods:
data[] <- sapply(data, func
Sorry, I should have added
library(gplots)
in the beginning of my code
On Sun, Jan 13, 2013 at 5:04 PM, Uwe Ligges
wrote:
>>
>> mycol <- colorpanel(n=3,"green","grey","red")
- - -
Peter K Davidsen | MSc, PhD stud. | Centre for Systems Biology | Univ.
of Liverpool | Crown Street | L69 7ZB, U
On 12.01.2013 23:40, Peter Davidsen wrote:
Dear List,
I'm trying to generate a simple heatmap that has each row and column
separated by a black line. However, for some reason this only happens
for the first and last color. The middle color in my colorpanel()
command has an addition horizontal
Use the col= argument to the heatmap() function to specify the three
colors you want. For example:
x <- matrix(rnorm(50), ncol=5)
heatmap(x, col=1:3)
Jean
furor wrote on 11/14/2012 03:31:42 AM:
>
> Hi all,
>
> I've made a heatmap using '-', '=' and '+' as possible values. H
On Fri, 28 Sep 2012, David Winsemius wrote:
On Sep 28, 2012, at 4:52 PM, David Winsemius wrote:
On Sep 28, 2012, at 3:16 PM, Nick Fankhauser wrote:
Hello R-Users!
I'm using a heatmap to visualize a matrix of values between -1 and 3.
How can I set the colors so that white is zero, below ze
On Sep 28, 2012, at 4:52 PM, David Winsemius wrote:
>
> On Sep 28, 2012, at 3:16 PM, Nick Fankhauser wrote:
>
>> Hello R-Users!
>>
>> I'm using a heatmap to visualize a matrix of values between -1 and 3.
>> How can I set the colors so that white is zero, below zero is blue of
>> increasing in
On Sep 28, 2012, at 3:16 PM, Nick Fankhauser wrote:
> Hello R-Users!
>
> I'm using a heatmap to visualize a matrix of values between -1 and 3.
> How can I set the colors so that white is zero, below zero is blue of
> increasing intensity towards -1 and above zero is red of increasing intensity
On May 13, 2012, at 11:23 AM, li li wrote:
Dear all,
I have a data set which is 100 \times 100 matrix.
I made a heatmap of the data. The xlim and ylim
are both shown to be c(0,1). I want to make both the
xlim and ylim to be c(0,100). So the heatmap correspond to
the 100 \times 100 locations.
Thanks!
-Steve
-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Thursday, April 26, 2012 9:28 AM
To: Steven Wolf
Cc: r-help@r-project.org
Subject: Re: [R] Heatmap fidelity
On 26/04/2012 9:01 AM, Steven Wolf wrote:
> I'm having a problem when using
On 26/04/2012 9:01 AM, Steven Wolf wrote:
I'm having a problem when using heatmap. Even though the diagonal of my
matrix is all the same value, the diagonal of my heatmap is not all the same
color. Any suggestions?
heatmap() rescales the matrix by default. Use
heatmap(abs(psim), scale="none
example(heatmap.2) works for me, hence it is either your data, your
version of some package or your version of R that causes the problems,
we do not have information of any of these although the posting guide
asks you to provide this for each posting. So we cannot help.
Uwe Ligges
On 29.11.2
not sure about gplots, but the one in base R should work well if you
specify the scaling method to be 'none':
heatmap(a4[1:40, ], Rowv=NA, Colv=NA, col=c("grey", "blue", "purple",
"red"), scale='none')
Regards,
Yihui
--
Yihui Xie
Phone: 515-294-2465 Web: http://yihui.name
Department of Statisti
I wrote this function (borrowing heavily from an example from Longhow Lam)
heatplot = function(x,y,z,bgcol="#777044",coltype='heat', ccex = 1.5,
circles=TRUE, ...){
#browser()
layout(matrix(c(1, 2, 3), nc=3), widths=c(7, 1, .5))
## create the scatterplot withdifferent color
Hi Sarah,
To me, the heatmap function calculates "density value" for each grid
of the heatmap automatically from the input matrix. In my case, I
already got the "density value" as a vector, say Z. I want to plot a
heat map with x and y as is axsis and z values as the "density" of
grid. I
You mean like the examples in help("heatmap") ?
On Tue, Sep 6, 2011 at 1:20 PM, Jinrui Xu wrote:
> Hi everyone,
>
> I have three numerica vectors: x, y, z. I want to plot a heatmap or surface
> plot of z against x and y. Is there any package for this? If possible,
> please drop me several lines o
"r-help@r-project.org"
Sent: Tuesday, 9 August 2011, 1:32
Subject: Re: [R] heatmap is producing unwanted horizontal and vertical lines?
Is it this?
https://stat.ethz.ch/pipermail/r-devel/2011-July/061540.html
Try a recent version of R 2.13.1 patched
> Hi Pete,
>
> I thought it
d and
that was giving the same result as well.
What I'm wanting are blocks together without the white lines going through but
just cant seem to find a way to do that?
Best regards,
Col.
From: Peter Morgan
To: Colin Ford
Sent: Monday, 8 August 2011, 1
'm wanting are blocks together without the white lines going through
> but just cant seem to find a way to do that?
>
> Best regards,
> Col.
>
>
>
> From: Peter Morgan
> To: Colin Ford
> Sent: Monday, 8 August 2011, 14:37
&
Search terms likely to be productive: white lines anti-aliasing pdf
(or variations there within)
--
David
Best regards,
Col.
From: Peter Morgan
To: Colin Ford
Sent: Monday, 8 August 2011, 14:37
Subject: Re: [R] heatmap is producing unwanted horizontal and
vertical l
nt: Monday, 8 August 2011, 14:37
Subject: Re: [R] heatmap is producing unwanted horizontal and vertical lines?
Hi Col,
Without seeing your data and the heatmap
you are plotting it is hard to tell what is going on. Are the NAs in any
pattern? NAs appear in heatmap as the background colour which
That what I did, I replaced the -infinite with lowest number I got from my
data set.
I'm not sure this kind of data manipulation is allowed in a publication
--
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Sent from the R help mailing
On Jul 18, 2011, at 3:34 PM, rebioman wrote:
Hi all,
new to this forum
I'm try to using R to draw a heatmap of my RNA-seq data
before doing that I did a log2 transformation of my data and produce
a lot
-inf in the matrix
when I try to use the heatmap function, it seems can not deal with
th
Thanks for the tip on the limit attribute on scale_fill_gradientn.
I'll check out mencoder and let you know if I use your code for the movie.
Cheers
--
View this message in context:
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Sent from the R help mailing li
On Tue, Jun 14, 2011 at 19:56, idris wrote:
> Follow up question: My data contains x, y, height, and day.
>
> I want to create the heatmap for each day, keeping the color coding
> consistent.
>
> I've created an example with 2 days, and you can see the charts below.
>
> Notice that the legend chan
On 06/14/2011 08:53 PM, Agustin Lobo wrote:
Hi!
I'm displaying a contingency table with heatmap():
svm.predPix.tabla
svm.predPix CC DD LL NN NN2
CC 22 0 3 8 3
DD 0 27 0 1 0
LL 1 1 90 3 7
NN 2 0 1 11 4
NN2 0 0 5 1 20
h
Thanks for your help!
Follow up question: My data contains x, y, height, and day.
I want to create the heatmap for each day, keeping the color coding
consistent.
I've created an example with 2 days, and you can see the charts below.
Notice that the legend changes from day 1 to day 2. How can I
Hi,
Try this
ggplot(df, aes(x,y)) + geom_tile(aes(fill=height), colour="white") +
scale_fill_gradientn(colours = c("red", "gold", "green")) +
geom_text(aes(lab=height))
HTH,
baptiste
On 14 June 2011 07:12, idris wrote:
> I have a dataframe df with columns x, y, and height. I want to create a
Brilliant, that's exactly what I needed. Thank you. The axis labels are
duplicated on top and the bottom now though, but I'm sure there's a way to
suppress them from appearing.
On Jun 3, 2011, at 11:24 AM, David Winsemius wrote:
>
> On Jun 3, 2011, at 9:26 AM, Mark Aquino wrote:
>
>> Yes I u
On Jun 3, 2011, at 9:26 AM, Mark Aquino wrote:
Yes I understand what ? means, I meant is it possible to use
this function (as an argument) with heatmap.2, but I learned I can
use add.expr=mtext() to do that. However I'm not simply trying
to add more text to the graph but rather move
Yes I understand what ? means, I meant is it possible to use this
function (as an argument) with heatmap.2, but I learned I can use
add.expr=mtext() to do that. However I'm not simply trying to add more
text to the graph but rather move the display of the x-axis labels from the
bottom of
On Jun 2, 2011, at 4:08 PM, Mark Aquino wrote:
Hi,
I have what would seem to be a very simple problem but have been
unable to find any way to go about solving it:
I am using heatmap.2 to create a heatmap and by default the x axis
label is at the bottom of the heatmap, I simply want to move
I am intesrested by your heatmap function (allowing matrix in ColSideColors
option). Can you give your complete code of your function? thanks
--
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_
Hi Chakravarthy,
[dont forget to Cc the list for useRs with the same Q.]
If you're trying to reuduce the isze of your row or column labels, i
think the following arguments of heatmap.2 {gplots} is what you want to
adjust- 'cexCol' and 'cexRow'.
Specifically on my question that you ask about,
> Date: Wed, 9 Feb 2011 12:18:57 -0500
> From: yanliu...@gmail.com
> To: r-help@r-project.org
> Subject: [R] heatmap-how to change the order of the rows (genes)
>
> Hi,
>
> I have a question about the heatmap dendrogram in R. I loaded my data
> matrix in
Hi,
On Wed, Feb 9, 2011 at 12:18 PM, yan liu wrote:
> Hi,
>
> I have a question about the heatmap dendrogram in R. I loaded my data
> matrix in command heatmap(), and it gave me a heatmap accordingly, and the
> rows (genes) also were clustered accordingly. But now I don't want the
> genes clust
It's hard to know without a minimal reproducible example, but you
probably want scale_fill_gradient or scale_fill_gradientn.
Hadley
On Thu, Oct 28, 2010 at 9:42 AM, Struchtemeyer, Chris
wrote:
> I am very new to R and don't have any computer program experience
> whatsoever. I am trying to gener
sorry, typo:
> heatmap.2(x,col=colorRampPalette(c("blue","lightblue","darkgray","darkgray","yellow","red"),space="Lab"),at=c(-6.01,6.01,51))
> heatmap.2(x,col=c("blue","lightblue","darkgray","black","darkgray","yellow","red"),at=-3:3*2)
should be read as
heatmap.2(x,col=colorRampPalette(c("blue
Hi Rashid,
you may have a look at the colorRampPalette-function, along with the
"at" argument oh heatmap.2
x<-matrix(runif(100,-6,6),nrow=10)
heatmap.2(x,col=colorRampPalette(c("blue","lightblue","darkgray","darkgray","yellow","red"),space="Lab"),at=c(-6.01,6.01,51))
# or just using the colors you
I see now my error, several in fact:
The 'breaks' specified need to be of a similar range to the data range,
and they should be equally spaced.
So in my example:
breaks = seq(0, 0.2, 0.001)
If one needs uneqaully spaced coloring, as i do, then this is achieved
by specifying the approprate c
On 03/16/2010 04:06 PM, Tim Smith wrote:
> Hi,
>
> I wanted to make more than one side color bar.
The function heatmap.plus (library: heatmap.plus) can do that, just
combine the different color vectors with cbind(col1,col2). Unfortunately
the arguments required for heatmap, heatmap.2 and heatmap
data(warpbreaks) ## given two factors
coplot(breaks ~ 1:54 | wool * tension, data = warpbreaks,
col = "red", bg = "pink", pch = 21,
bar.bg = c(fac = "light blue"))
##
conditionalplot
#
If anyone is interested, I solved the problem by modifying the lhei parameter
(if ColSideColors is used, lwid for Row..) and making it parametric:
lhei=c(lhei[1], 0.1*noan, lhei[2])
where noan is an additional parameter passed to the function that specifies
the number of annotations.
best,
j
-
also, can you point me to some example of how to omit colors from a palette
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__
R-help@r-project
thanks,
I think I got the color ranges down, however, I just realized that the
colors don't match the data. When I execute:
grad <- ifelse(randMat > 5,yelPal,ifelse(randMat<1.5,redPal,bluPal))
the grad matrix contains the correct hex codes corresponding to the randMat
data matrix but when I
as a followup, I tried using the rainbow function to create the gradients but
is there a way to do a "reverse" rainbow, ie. normally if I do:
pie(rep(1,6), col=rainbow(6,start=0, end=.07))
I'll get a gradient from dark red to orangish but what if I want it to go
the other way
thanks
--
View t
evgeny55 wrote:
>
> I'm trying to create a heatmap with color ranges for different values in
> my matrix. For example:
> If x > 5 , use orange gradient
> if x < 1.5, use red gradient
> .
>
> Right now I have the following:
> orgPal<-brewer.pal(3,"Oranges")
> bluPal<-brewer.pal(3,"Blues")
This worked :o)
Thanks very much!
Liat wrote:
>
> Hi all,
> I'm trying to use heat.map to display some data.
> The data is originally in csv format and when I read it in R using
> read.table I get:
> a b c d e
> 1 A 1 1 1 1
> 2 B 1 0 1 1
> 3 C 0 1 0 1
> 4 D 1 1 1 0
> 5 E 1 0 0 0
> The problem
On Dec 10, 2009, at 10:19 AM, Liat wrote:
I have looked at the help for data.matrix. But didn't find a solution.
data.matrix only gets two arguments the data and a logical
rownames.force -
I have tried to change this logical to TRUE but that doesn't help.
Any advice would be greatly appreci
I have looked at the help for data.matrix. But didn't find a solution.
data.matrix only gets two arguments the data and a logical rownames.force -
I have tried to change this logical to TRUE but that doesn't help.
Any advice would be greatly appreciated.
Thanks!!
Liat wrote:
>
> Hi all,
> I'm tr
On Dec 10, 2009, at 8:25 AM, Liat wrote:
Hi all,
I'm trying to use heat.map to display some data.
The data is originally in csv format and when I read it in R using
read.table I get:
a b c d e
1 A 1 1 1 1
2 B 1 0 1 1
3 C 0 1 0 1
4 D 1 1 1 0
5 E 1 0 0 0
The problem is, that for heatmap I need
On Nov 23, 2009, at 10:02 AM, Daniel Brewer wrote:
Hello,
I am using heatmap.2 from the gplots library to plot a small
symmetrical matrix.
This is the command:
heatmap.
2
(tempHeat
,symm
=
T
,trace
="none",cexRow=0.7,cexCol=0.7,col="redgreen",density.info="none")
I have a couple
John Celniker wrote:
>
> ...
> when I try to change the breaks to:
>> br2
> [1] 0.000 0.5337751 1.0675502 1.6013253 2.1351003 3.000
> 3.500 4.000 4.500
> [10] 4.8039758
>
> I get the correct heatmap representation but the color key does not
> update correctly to reflect c
Try placing the column names into labCol and the rownames into labRow
e.g.heatmap.2(mat,dendrogram=c("none"),
Rowv=F, Colv=F, labRow = seq(-7.5,7.5,by=5), labCol=seq(-3,3,by=2))
Schalk Heunis
On Thu, Sep 17, 2009 at 3:53 PM, bioinformatics_guy wrote:
>
> Schalk,
>
> Thats a great function! The o
Schalk,
Thats a great function! The only question is, is it as flexible as
heatmap.2?
I figured out how to get it from rearranging the rows and columns but I
can't figure out how to label the rows and columns? What I like about the
heatmap.2 is that it gives a grid and histogram of the heatmap
Hi bioinformatics_guy
I think you are looking for the "image" function:
image(mat)
The heatmap.2 function does hierarchical clustering on rows and columns and
then orders the rows and columns according to the results of the clustering.
Image simply plots the matrix.
HTH
Schalk Heunis
On Thu, S
2009/7/21 Markus Mühlbacher :
> I tried to add white to the colors, but this did not change my problem. Still
> the values of the diagonal seem to be different from those occurring in the
> matrix. Or in other words all squares of the diagonal should have to SAME
> color!
If you can send me th
2009/7/21 Markus Mühlbacher :
> So just that I understand right. x and y are the scalings of the x and y axis
> and the matrix represents the color of the points at each gridpoint?
Precisely! Try ?image for more details.
--
Michael Knudsen
micknud...@gmail.com
http://lifeofknudsen.blogspot.com
since heatmap is a graphic image it needs the "graphics" library. you can see
these two in the examples for heatmap.
require(graphics); require(grDevices)
Markus Mühlbacher wrote:
>
> Dear R community!
>
> I am trying to create a heatmap based on the following data. As you can
> see the diago
2009/7/20 Markus Mühlbacher :
> Gives the attached image. Again I am missing the white diagonal. Is there
> some kind of sorting that I do not consider?
Maybe col=c("white",heat.colors(100)) will do the trick?
--
Michael Knudsen
micknud...@gmail.com
http://lifeofknudsen.blogspot.com/
2009/7/20 Markus Mühlbacher :
> What is my mistake?
I don't know about the heatmap function, but I have often used 'image'
with 'heat.colors' without any problems. There is a nice example here:
http://addictedtor.free.fr/graphiques/graphcode.php?graph=20
It should be fairly easy to fit your dat
Hi Chrysanthi,
Chrysanthi A. wrote:
Thanks a lot..! What exactly the sweep function is doing? Also, is there
a possibility instead of using the mean of the whole row to get only the
mean of a group of the row values? So the values in the matrix (heat
map) used in the comparison are z-scores
Thanks a lot..! What exactly the sweep function is doing? Also, is there a
possibility instead of using the mean of the whole row to get only the mean
of a group of the row values? So the values in the matrix (heat map) used in
the comparison are z-scores and not the intensities of the gene express
Hi Chrysanthi,
Chrysanthi A. wrote:
Hi,
I am analysing gene expression data using the heatmap.2 function in R and I
was wondering what is the formula of the "raw z-score" bar which shows the
colors for each pixel.
According to that post:
https://mailman.stat.ethz.ch/pipermail/r-help/2006-Septem
Dear Alex,
Take a look at the examples in
# Option 1
?heatmap
# Option 2
require(gplots)
?heatmap.2
HTH,
Jorge
On Mon, Jun 8, 2009 at 9:32 AM, Alex Roy wrote:
> Hello Group,
>How can I draw heatmap with variable names in the plot?
>
> Thanks
>
> Alex
>
>[[alterna
Couldn't you get that just by giving heatmap() the transpose of your
data?
> -Original Message-
> From: r-help-boun...@r-project.org
> [mailto:r-help-boun...@r-project.org] On Behalf Of Alex Roy
> Sent: Monday, June 08, 2009 9:32 AM
> To: r-help@r-project.org
> Subject: [R] Heatmap
>
>
Thanks Matthias! Exactly what I was looking for.
Paul
From: Matthias Kohl
Cc: r-h...@stat.math.ethz.ch
Sent: Wednesday, May 6, 2009 2:06:22 PM
Subject: Re: [R] Heatmap: draw horizontal line
Is
heatmap.2(mat,Rowv=NA,trace = 'none',key=F, add.expr
Is
heatmap.2(mat,Rowv=NA,trace = 'none',key=F, add.expr = abline(h =
c(3.5,5.5), lwd = 3))
what your are looking for?
hth,
Matthias
Paul Evans schrieb:
Hi,
I wanted to draw a heatmap with some horizontal lines. For example:
#-- code --
mat <- matrix(-1:1,7,9)
heatmap.2(mat,Rowv=NA
Antje wrote:
Hi Uwe,
thanks a lot for your answer! And thanks a lot to all others helping me
with this issue!
Uwe Ligges schrieb:
Antje wrote:
Hi Uwe,
I tried to explain my problem with the given example.
I don't see any documentation which tells me that the length of
"col.regions" sh
Hi Uwe,
thanks a lot for your answer! And thanks a lot to all others helping me with
this issue!
Uwe Ligges schrieb:
Antje wrote:
Hi Uwe,
I tried to explain my problem with the given example.
I don't see any documentation which tells me that the length of
"col.regions" should be one less
Antje wrote:
Hi Uwe,
I tried to explain my problem with the given example.
I don't see any documentation which tells me that the length of
"col.regions" should be one less than "at". (At least I assume now that
it should be this way...)
If it's equal or longer some colors (in the middle of t
The image function in base graphics does the same type of plot, just different
names and structure of the data (and the documentation says that the number of
breaks should be 1 more than the number of colors).
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermounta
Hi Uwe,
I tried to explain my problem with the given example.
I don't see any documentation which tells me that the length of "col.regions"
should be one less than "at". (At least I assume now that it should be this way...)
If it's equal or longer some colors (in the middle of the color-vector)
Antje wrote:
Hi there,
as I'm not sure to understand the coloring levelplot uses, I'm looking
for another easy way to create a heatmap like this:
library(lattice)
mat <- matrix(seq(1,5, length.out = 12), nrow = 3)
mat[1,2] <- 3.5
my.at <- seq(0.5,5.5, length.out = 6)
my.col.regions <- rain
Antje yahoo.de> writes:
> as I'm not sure to understand the coloring levelplot uses, I'm looking for
> another easy way to create a heatmap like this:
>
> library(lattice)
> mat <- matrix(seq(1,5, length.out = 12), nrow = 3)
> mat[1,2] <- 3.5
>
> my.at <- seq(0.5,5.5, length.out = 6)
> my.col.
Thanks James. That worked.
Tanuja
--- On Tue, 4/7/09, James W. MacDonald wrote:
From: James W. MacDonald
Subject: Re: [R] heatmap.2 no reordering of the columns and rows
To: "Tanuja Bompada"
Cc: r-help@r-project.org
Date: Tuesday, April 7, 2009, 8:02 AM
Hi Tanuja,
Tanuja Bom
Hi Tanuja,
Tanuja Bompada wrote:
Hi,
I need to generate a heatmap on a square matrix and wouldn't want to reorder the columns and the rows on the heatmap display.
I have used the options Rowv=NULL and Colv=NULL but doesn't seem to work. Following is a snippet of the heatmap function i am u
Check out http://cran.r-project.org/web/packages/RColorBrewer/index.html
On Wed, Mar 11, 2009 at 10:41 PM, Daren Tan wrote:
> I would like to visualize my data via heatmap so that the value range
> c(-2,2) corresponds to greenred(75). However, heatmap uses the min and
> max from my dataset instea
I played a little bit around and got the following solution which works for
now, though it seems to be too complicated to me.
If anybody else know another solution - please let me know!!!
library(lattice)
my.mat <- matrix(rnorm(800), nrow = 40)
colorFun <- colorRampPalette(c("yellow","red"))
I played a little bit around and got the following solution which works for
now, though it seems to be too complicated to me.
If anybody else know another solution - please let me know!!!
library(lattice)
my.mat <- matrix(rnorm(800), nrow = 40)
colorFun <- colorRampPalette(c("yellow","red"))
b
the heatmapCol function of package MKmisc might help ... try:
library(MKmisc)
example("heatmapCol")
Best
Matthias
Liu, Hao [CNTUS] wrote:
Dear All:
I tried to use heatmap.2 to generate hierarchical clustering using the
following command:
heatmap.2(datamatrix, scale="row", trace="none", col=g
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