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 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 play for
3 hours and can not resolve the problem.
Thank you,
Ding
--
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
Dear Sir,
Please help me solving the error occurring during the execution of the code
given below.
library("openxlsx")
library(gplots)
library("RColorBrewer")
rix <- read.xlsx(file.choose(), sheet = 1, colNames = TRUE,rowNames = TRUE)
rawdata <- data.matrix(rix)
colors =
c(seq(-2,-0.5,length=
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
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 and vertical line that I would like
to get rid
Hi ,
I am trying to plot a heatmap with a correlation matrix and trying to
highlight significant correlations .
i am using
my matrix d874n has 78 columns
ex2<-corAndPvalue(data.matrix(d874n),use = "pairwise.complete.obs")
##creating a matrix of true false using p values
sig<-ex2$p<0.05
nx=78
ny=7
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
Hi
I used to make heatmaps using following commands but now some thing
has changed as I get
library(gplots)
heatmap.
2(qtl.map,Rowv=F,dendrogram="column",col=colorRampPalette(c("blue","lightblue","black","black","yellow","red")),breaks=seq(-4.01,4.01,length.out=51),
density.info="none", )
follow
I am using attributes colsep and sepwidth from heatmap.2 function,
however when using larger values for sepwidth the following columns are
not moved to the right but the seperator is covering the column(s) with
a white bar and the column labels and ColSideColors remain at their
positions, is th
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,
Dear List!
I'm using R2.8.1 with windows. In my Analysis I use the heatmap.2
function. That works quite well except there is one little detail I
can't change. I like to make the key a bit smaller than default. So I
pass in "keysize=1" into the function. The key is smaller, but the
main and the x y
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
Esteemed R-users,
heatmap.2() is yielding an inappropriate key based on my colors and
break-points.
In the reproducible example below, the key is inappropriate (to me) because-
1. 'Orange' is simply not represented in the key, despite its prescence
in the heatmap.
2. The proportions of the k
Esteemed R user's,
I'm struggling to achieve some details of a heatmap using heatmap.2():
1. Change label locations, for both rows & columns from the default
right & bottom, to left and top.
Can this be done within heatmap.2()? Or do i need to suppress this
default behavior (how) and call a ne
Hi,
Does heatmap.2 function combine all variables into a single overall measure of
dissimilarity (regardless of dissimilarity) between two observations as
explained in The elements of statistical learning, Hastie et al, 2001, pp457?
Does this function calculate the dissimilarity between observat
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
Hi,
I wanted to make more than one side color bar. For example, I can make one side
color bar (col1) with the following code:
---
library(gplots)
mat <- matrix(sample(1:100,40),nrow=5)
class1 <- c(rep(0,4),rep(1,4))
col1 <- ifelse(class1 == 0,"blue","red")
class2
also, can you point me to some example of how to omit colors from a palette
--
View this message in context:
http://n4.nabble.com/heatmap-2-color-range-tp1293498p1311031.html
Sent from the R help mailing list archive at Nabble.com.
__
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")
Hi,
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")
redPal<-brewer.pal(3,"Reds")
grad
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
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 of questions:
1) The range is from -0.2 to 0.4 and the colour scheme I
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
Hi folks,
I have been working with the ellipse library and trying to use the
heatmap.2 function. I have called the function as follows
hh <- heatmap.2(DATA, Rowv= F, trace = "none",
colsep=seq(1, 4), rowsep = seq(1,dim(GENES)[1]), col =
brewer.pal(9, "YlOrRd"),
lmat=rbind( c(3, 4,0)
Hi folks,
I have been working with the ellipse library and trying to use the
heatmap.2 function. I have called the function as follows
hh <- heatmap.2(DATA, Rowv= F, trace = "none",
colsep=seq(1, 4), rowsep = seq(1,dim(GENES)[1]), col =
brewer.pal(9,
"YlOrRd"),
lmat=rbind( c(3, 4,
Hi folks,
I have been working with the ellipse library and trying to use the
heatmap.2 function. I have called the function as follows
hh <- heatmap.2(DATA, Rowv= F, trace = "none",
colsep=seq(1, 4), rowsep = seq(1,dim(GENES)[1]), col = brewer.pal(9,
"YlOrRd"),
lmat=rbind( c(3,
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
I have a file of the following form
-11 -10 -9 -8
-10 -9 -8 NA
-9 -7NA NA
-8NA NA NA
So basically a NxN matrix of log scores. I want to get a heatmap of these
log scores but I'm having a problem.
I'm using the following code
library(gplots)
data=read.table("filein.txt",header=
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
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-September/113598.html, it
is the
(actual val
heatmap.2() from gplots does not seem to accept a dendrogram produced by
the stats package function heatmap():
>
testHeatmap=heatmap(test[,1:40],Colv=NA,col=bluewhitered(256),labRow=testL,keep.dendro=TRUE)
# draws expected image
# to prove this dendro is OK, redraw with same function:
>
heat
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
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 using.
args <- commandArgs();
inpu
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
Dear All:
I tried to use heatmap.2 to generate hierarchical clustering using the
following command:
heatmap.2(datamatrix, scale="row", trace="none", col=greenred(256),
labRow=genelist[,1], margins=c(10,10), Rowv=TRUE, Colv=TRUE)
datamatrix is subset of a RMA normalized data subset by a genelis
ject.org
Subject: [R] heatmap.2 and three colours for specific rangesþ
Hi,
I hope to show a heatmap with thre colours, no gradation. How to specify
heatmap.2 to map "green" for values less than -1, "gray" for values between
-1 and 1, and "red" for values greater than 1
Hi,
I hope to show a heatmap with thre colours, no gradation. How to specify
heatmap.2 to map "green" for values less than -1, "gray" for values between
-1 and 1, and "red" for values greater than 1 ?
Thanks
[[alternative HTML version deleted]]
__
Hi, there,
I am planning to use heatmap.2 function to draw some heatmaps. However, I
don't want to use default set manhattan distance and complete linkage in
heatmap.2. How should I change parameters distfun and hclustfun? Thank you.
ys
[[alternative HTML version deleted]]
_
RobertsLRRI wrote:
Hello
does anyone know what algorithm is used to produce the hierarchical
clustering in the gplots package using the function heatmap.2? I think it
may be the complete linkage clustering algorithm, but I can't find a source
that seems reliable.
Did you look at the help page
Hello
does anyone know what algorithm is used to produce the hierarchical
clustering in the gplots package using the function heatmap.2? I think it
may be the complete linkage clustering algorithm, but I can't find a source
that seems reliable.
Thank you and sorry if I posted this in the wrong
Dear Peter,
the call works for me; e.g.
x <- matrix(rnorm(100), ncol = 4)
heatmap.2(x, dendrogram="none", Colv = FALSE, Rowv = FALSE)
There seems to be something wrong with your matrix z ...
Best,
Matthias
Peter Scacheri wrote:
Thanks Matthias,
I tried that, but received the following error
heatmap.2(z, col = greenred(100), dendrogram = "none", Rowv = FALSE)
NULL isn't one of the accepted values for the dendrogram argument. See
?heatmap.2
Best,
Jim
Peter Scacheri wrote:
Using the heatmap.2 function, I am trying to generate a heatmap of a 2
column x 500 row matrix of numeric
Thanks Matthias,
I tried that, but received the following error message:
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)
-Peter
At 10:18 AM +0200 5/15/08, Matthias Kohl wrote:
Dear Peter,
heatmap.
Dear Peter,
heatmap.2(z, dendrogram = "none", Rowv = FALSE, Colv = FALSE)
should do what you want.
Best,
Matthias
Peter Scacheri wrote:
Using the heatmap.2 function, I am trying to generate a heatmap of a 2
column x 500 row matrix of numeric values. I would like the 1st
column of the matrix
Using the heatmap.2 function, I am trying to generate a heatmap of a
2 column x 500 row matrix of numeric values. I would like the 1st
column of the matrix sorted from the highest to the lowest values -
so that the colors reflected in the first column of the heatmap (top
to bottom) go from red
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