Displaying 20 results from an estimated 5000 matches similar to: "Problems with heatmap.2 in the gregmisc package"
2004 Sep 02
3
Problems with heatmap.2
Hi
When I give the command:
>
heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="row
",trace="none",col=greenred.colors(79))
The resulting heatmap has re-ordered my columns! This is time-course
data, and I don't want my columns re-ordered! Note from the help:
Rowv: determines if and how the _row_ dendrogram should be
reordered.
2006 Feb 11
2
heatmap.2 in gplots (PR#8587)
Full_Name: Shane Neph
Version: 2.2.1
OS: mac os x
Submission from: (NULL) (71.113.43.247)
While I found the names of the package authors and maintainer, I was
unsuccessful in finding any contact information.
The preliminary documentation for heatmap.2 is inconsistent in at least a couple
of places when discussing the suppression of one or more dendrograms (and
column/row ordering in general).
2009 Apr 07
2
heatmap.2 no reordering of the columns and rows
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();
inputfile <- args[2]
imgfile <- args[3]
bitmap(imgfile, height=15, width=15, res=100,
2008 May 14
4
Heatmap.2 - eliminate cluster and dendrogram
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 to green.
After sorting the matrix (z), I tried the following command, but the
data remains
2005 Aug 22
2
problem building dendrograms to use with heatmap()
Hi,
I'm trying to build dendrograms to pass to heatmap().
The dendrograms I build plot properly, but when I pass them to heatmap() I get
the error message "row dendrogram ordering gave index of wrong length" (see
output log below).
I looked in the code of heatmap() and saw that the error was due to a NULL
return value from order.dendrogram(), which in turn got a NULL return value
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
2004 Jul 21
2
Cutting heatmap dendrogram
Hello,
I've been clustering my data using hclust and cutting the resulting tree
with cutree. Separately, I visualize the clusterings with heatmap. Is it
possible to have the dendrogram on the heatmap reflect the cutree results?
That is, instead of having one large dendrogram, it would have 4 or 25 in
the example below. Any guidance on if that's possible or not, and what
kinds of
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",
2010 Jul 19
1
heatmap.2() yielding an inappropriate key?
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 key are clearly out, ie., my largest bin, (0.1
- 0.2) is half the range, but this bin (colored
2011 Jun 30
1
heatmap documentation typo
Under Details, the documentation says "[if Rowv or Colv] is 'NULL',
_no reordering_ will be done for the corresponding side." In fact, as
explained elsewhere in the documentation, 'NA' is required, not
'NULL'.
An anonymous expert suggested that I should attach an svn diff file to
this report, so I will.
JD
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2003 Oct 17
1
heatmap function
Hi all,
By default, the heatmap function gives an image with a dendrogram added
to the
left side and to the top. Is it possible to only add the dendrogram to
the left side
and let the order of the columns unchanged ?
I tried
heatmap(mat, col=rbg,Rowv=res.hclust$order,Colv=1:dim(mat)[[2]]).
In this case, the order of the columns are unchanged but a dendrogram
is added to the top. How can I
2008 Sep 25
2
levelplot/heatmap question
Hello!
I have data containing a large number of probabilities (about 60) of nonzero
coefficients to predict 10 different independent variables (in 10 different
BMA models). i've arranged these probabilities in a matrix like so:
(IV1) (IV2) (IV3) ...
p(b0) p(b0) p(b0)
p(b1) p(b1) p(b1)
p(b2) p(b2) p(b2)
...
where p(b1) for independent variable 1 is p(b1 !=
2007 Aug 23
1
figure-definition and heatmap question
Hello,
I have two questions. I'd like to visualize data with a heatmap and I have the
following testcase:
x <- rnorm(256)
nx <- x + abs(min(x))
nnx <- 255/max(nx) * nx
x <- matrix(nnx, 16, 16)
rownames(x) <-
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
2009 Aug 24
1
Saving heatmaps as PDFs
Hi,
I'm trying to save heatmaps as PDFs. However, the PDF version of the
heatmaps (Heatmap_CAFvsTNF_run2.pdf) is blurred when compared to its
counterpart, which was saved manually by using the software
"Grab" (Heatmap_CAFvsTNF_run2.tiff).
-----R code--------
sample_output <- "stroma_run2"
filename <-
2004 Sep 07
1
gridBase and heatmap
I would like to use gridBase to place four separate heatmaps (actually,
a stripped-down heatmap.2 from ght gregmisc package that contains only
the "image" part) into four different viewports. I can get the
placement correct, but I keep 'losing' the previous plot. Any
suggestions?
Here is some quick example code trying to put a heatmap into the left
viewport and then
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
2007 Dec 06
2
hclust in heatmap.2
Dear list,
I am using heatmap.2(x) to draw a heatmap. Ideally, I want to the matrix
x clustered only by columns and keep the original order of rows unchanged.
Is there a way to do that in heatmap.2()?
Thanks a lot! Any suggestions will be appreciated!
Best,
Allen
[[alternative HTML version deleted]]
2004 Jan 04
5
Analyzing dendograms??
I have used heatmap to visualize my microarray data. I have a matrix of
M-values. I do the following.
#The distance between the columns.
sampdist <- dist(t(matrix[,]), method="euclidean")
sclus <- hclust(sampdist, method="average")
#The distance between the rows.
genedist <- dist(matrix[,], method="euclidean")
gclus <- hclust(genedist,
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