Displaying 20 results from an estimated 1000 matches similar to: "row-side color bars do not reverse properly in heatmap (PR#7972)"
2005 Jun 29
1
(PR#7972) row-side color bars ... in heatmap
Hi Kevin,
>>>>> "krc" == krc <krc at odin.mdacc.tmc.edu>
>>>>> on Mon, 27 Jun 2005 21:55:37 +0200 (CEST) writes:
krc> Full_Name: Kevin R. Coombes
krc> Version: 2.1.0
krc> OS: Windows XP
krc> Submission from: (NULL) (143.111.224.169)
krc> When revC = TRUE and RowSideColors is set to a list of
krc>
2012 Feb 28
1
Unexpected behaviour for RowSideColors in function heatmap
Hello,
I have come across some unexpected behaviour of the function heatmap in the stats package. This looks like a bug to me, but I might have misunderstood something.
When calling the function in symmetric mode, the ColSideColors are plotted correctly, but RowSideColors appear in reverse order. This code (modified from the example on the help page) demonstrates the problem:
cU <-
2009 Jul 21
1
problem with heatmap.2 in package gplots generating non-finite breaks
I have written a wrapper for heatmap.2 called
heatmap.w.row.and.col.clust which auto-generates breaks using
breaks<-round((c(seq(from=(-20 * stddev), to=(20 * stddev))))/20,
digits = 2) #(stddev in this case = 2.5)
This has always worked well in the past but now I am getting an error
that non-finite breaks are being generated. Drilling down, it seems
that my wrapper is generating finite
2011 Oct 18
0
heatmap
Dear R users, need help with my heatmap. I will really approciate some help.
Given the matrix:
> head(x)
A B C D time
[1,] 0 8 0 0 1
[2,] 0 160 0 0 2
[3,] 0 175 0 0 3
[4,] 0 253 0 0 4
[5,] 79 212 0 0 5
[6,] 6 105 0 0 6
and call:
##------------ Heatmap --------------
library(RColorBrewer)
rc <- grey((nrow(x):1)/nrow(x))
heatmap(data.matrix(x[,1:4]),
2006 May 16
0
reordering materix presentation in heatmap.2 in the 'gplots' library
Dear R users,
I'm trying to create images of 2 symmetrical matrices using heatmap.2 of the 'gplots' library. Both matrices have the same row and column names
For the first matrix I'm using the default clustering and column denrogram options:
heatmap.2(Matrix1, symm=T, breaks=20, col=rich.colors(19), main="matrix1", density.info="histogram",
2004 Dec 15
1
hclust and heatmap - slightly different dendrograms?
Good afternoon,
I ran heatmap and hclust on the same matrix x (strictly, I ran
heatmap(x), and hclust(dist(t(x))), and realized that the two
dendrograms were slightly different, in that the left-right
arrangement of one pair of subclusters (columns) was reversed in the
two functions (but all individual columns were grouped correctly).
Looking through the code for heatmap as a most definite
2006 Jan 23
1
lines() in heatmap()
Hello!
I looked for help through google and the help-files and spend several
hours with trial and
error, but didn't find a correct way.
It's all about lines in a heatmap to separate different data block from
each other to underline
the significance of the found clusters!
The heatmap is build like that:
heatmap(X, Rowv=NA, Colv=NA, symm=TRUE, cexRow=0.3, cexCol=0.3)
I switched the
2012 Jun 06
0
heatmap.2 clustering and adding add.expr
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=78
makeRects <- function(tfMat,border){
cAbove =
2013 Jan 12
3
heatmap.2 problem
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 off. Any suggestions?
#my code below
my.matrix <- cbind(func.1 =
2011 Mar 29
0
Fwd: comparing heatmaps
Thanks Tom.
heatmap.2(mat, Rowv=NA, Colv=NA, col=redgreen, breaks=seq(-1,1,by=0.01), symm=TRUE, trace="none", dendrogram="none")
that did the trick :)
Begin forwarded message:
From: "Leja, Thomas"
Date: 29 March 2011 03:47:59 GMT+01:00
To: "Benton, Paul"
Subject: Re: [R] comparing heatmaps
Yep, you have to specify the range for colours.
I usually
2014 Sep 04
1
gplot heatmaps: clustering according to rowsidecolors + key.xtickfun
Hi there,
I have two questions about heatmap.2 in gplot.
My input is a simple square matrix with numeric values between 75 and
100 (it is a similarity matrix based on bacterial DNA sequences).
1. I can sort my input matrix into categories with rowsidecolors (in
this case, very conveniently by bacterial taxa). I do a clustering and
reordering of my matrix by Rowv=TRUE (and
2010 Mar 03
1
Heatmap reordering of dendrogram to hierarchical clustering
Dear list members,
I have been using R to create a heatmap where my data has continous
variables from 0 to 100.
When I create the heatmap, although the branches are correct, they do not
order themselves so that the row with the most zeros is at one end and the
row with the most 100s is at the other, which is what I would like them to
do, so as to create a colour gradient down the graphic.
I have
2011 Mar 27
3
comparing heatmaps
Dear all,
I've been trying to find how to compare tow different heatmaps but I'm having trouble getting the colors bar to be the same. I'm doing something like the following:
library(gplots)
dat<-cor(matrix(rnorm(100, m=10), nrow=10))
mat<-cor(matrix(rnorm(100), nrow=10))
dev.new()
heatmap.2(mat, Rowv=NA, Colv=NA, col=redgreen(75), symm=TRUE, trace="none",
2009 Sep 21
1
Specific criteria for color palette using heatmap.2
I'm trying to display the probability space of a function and wanted to see
specifically where the maximum posterior probability is.
data=read.table("PosteriorData",header=F)
mat=as.matrix(data)
heatmap.2(mat/max(mat,na.rm=T),dendrogram=c("none"),trace=c("none"),
Rowv=F,Colv=F,labRow=3*c(10:-10),labCol=3*c(-10:10),symm=T,col=rainbow(100))
As the
2012 Mar 20
0
labeling rows in heatmap.2
how can i put the row labels on the left hand of the heatmap in heatmap.2?
abnr<-structure(c(1, 0.678622097406395, 0.670294749652918,
-0.0016314464654279,
-0.000519068106572792, 0.199581999119988, -0.0106623494189115,
0.0840111691399559, -0.0461494399639137, 0.249279171677728, NA,
1, 0.757114062773504, 0.0352642759270137, -0.0255518450373996,
0.0943268190664674, -0.0536269679247722,
2006 Feb 02
0
Heatmap.2 axes question
I'm suppressing the labeling of my rows and columns in heatmap.2 using the
commands:
labRow = " ", labCol = " "
But I'd like to annotate them again using the axis command:
axis(1, at=seq(500, 1000, 500))
mtext("Group 1", "Group 2")
For some reason however it appears that the axis command is having no
effect. My complete
2010 Feb 23
2
heatmap.3
Hello again,
lately I have been playing a lot with heatmap functions,
in particular I complemented heatmap.2 with a nice feature from
heatmap.plus,
i.e. the possibility of assigning a matrix to ColSideColors so to take into
account more annotations.
Below is the code I introduced in heatmap.2, everything else is maintained
equal to heatmap.2:
if (!missing(ColSideColors)) {
#if
2012 Feb 27
1
row names of a heatmap on left hand side
Hello R Gurus,
I have a matrix for which I am doing a heatmap using heatmap.2. I want to
put the rownames on the lefthand side instead of the right side of the
heatmap. how can i put the rownames on left hand side: I have already tried
axis but could not make it work
ccc<-structure(c(1, 0.283300333755851, 0.237863231117007,
0.0148696794159253,
-0.0780756406815149, -0.106161465097659,
2007 Sep 05
1
problem formatting and positioning title in heatmap
I am using heatmap with the arguments below. The title size stays the
same no matter what I set cex.main to. Is this expected? Can I adjust
the title size in heatmap?
Also, the position of the main title is at the very upper edge of the
output and if I use a "\n" to stack the title the upper line is out of
bounds and doesn't show up.
I am outputting to pdf.
Any help? Thanks,
2011 Mar 02
2
clustering problem
Hi,
I have a gene expression experiment with 20 samples and 25000 genes each.
I'd like to perform clustering on these. It turned out to become much faster
when I transform the underlying matrix with t(matrix). Unfortunately then
I'm not anymore able to use cutree to access individual clusters. In general
I do something like this:
hc <- hclust(dist(USArrests), "ave")