Displaying 20 results from an estimated 8000 matches similar to: "heatmap"
2008 May 28
0
interactive heatmap dendrogram locator layout grid package
Hello,
I would like to display a heatmap with dendrograms and allow the user to click
on either dendrogram to choose a sub-dendrogram.
The function heatmap() uses layout() and image() and the plot method of
dendrogram to plot the heatmap and dendrograms, but if locator() is then called
and the user clicks, the coordinates returned from locator() are with respect to
the last thing plotted (e.g.,
2007 Apr 25
1
heatmap and phylogram / dendogram ploting problem, ape package
I am having trouble displaying a dendrogram of evolutionary
relationships (a phylogram imported from the ape package) as the
vertical component of a heatmap, but keeping the hierarchical
clustering of the horizontal component. The relationships of the
vertical component in the generated heatmap are not that of the
dendrogram, although the ordering is.
In more detail, I am attempting to generate
2009 Sep 12
0
consistent results with heatmap.2
Hi,
I am trying to create a heatmap with some specific requirements. Specifically,
I need to be able to center the color-scale around 0, and I need to truncate the
data so that a few extreme values do not cause the rest of the heatmap to appear
black (on a red/green scale).
After reading through and experimenting with heatmap, heatmap.2, heatmap_plus,
and heatmap_2, I believe heatmap.2 will
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 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).
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
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",
2003 Nov 03
0
mva Hclust, heatmap and plotting functions
Hi All
Not sure if this a bioconductor question or general R mailing list
so apologies if this has gone to the wrong one.................
When plotting dendrograms created by hclust you can "identify" clusters
by clicking on the graphics and returning a list of what is contained in
each cluster. However I'd like to be able to "zoom in" on specific
clusters and plot
2006 Mar 09
1
Identifying or searching for labels in a hclust/dendrogram/heatmap
Hi
Sorry if this is in the help :-S
I've looked at example(dendrogram) and though it gives some indication of what I want, it doesn't do all.
OK, so here is what I want to do: draw a tree, and then have an action, on user-click, to either draw a sub tree or a plot of the data. I also want users to be able to search for a particular label and have it highlighted on the tree, say in
2004 Jan 03
0
error "evaluation nested too deeply" {was "Heatmap"}
I'm diverting this to the more appropriate mailing list, R-help,
since heatmap() is standard R function.
>>>>> "Johan" == Johan Lindberg <johanl at kiev.biotech.kth.se>
>>>>> on Fri, 02 Jan 2004 10:04:14 +0100 writes:
Johan> I am trying to plot a matrix of m-values in a heatmap
Johan> with "average linkage". The rows
2010 Sep 17
1
Question: how to obtain the clusters of genes (basically the ones in the row dendrograms) from an object obtained by heatmap.2 function
Hello R-Helpers,
I have a question about extracting the clusters of genes after we make the
heatmap (say ht4) using the heatmap.2 function. Basically, I want to get the
clusters which are shown as row dendrogram in the heatmap.
I understand that ht4$rowDendrogram is an object of dendrogram and it
containes details of all the nodes and branches, but lets say I want to know
the number of clusters
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
2009 Aug 17
0
heatmap and dendrogram
Dear all,
I generated a heatmap with the heatmap() function with the default
"complete" linkage method, but when I add the argument
Rowv=as.dendrogram(hclust(dist(matrix), method="complete")),
The dendrogram generated is different from the dendrogram produced by
heatmap() with default settings. Could someone kindly point out where my
mistakes are?
P.S. When I did
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>
2004 Aug 25
1
Problems with Heatmap
Hi
I am having some problems getting my heatmap to be the right size! Let
me explain. I am experienced at getting an hclust or a dendrogram
object to be the right size.
For example, I have a dataset which has 4000 rows, which I clustered
using hclust and I wanted to plot it as a horizontal dendrogram. So I
used jpeg(), set the image height to be 4000 and plotted the dendrogram
and got the
2011 Apr 11
1
heatmap clustering dendrogram export
Hi,
I am a beginner for R.
I had use gplots to generate a heatmap as following:
>heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE,
trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2,
cexCol=0.6)
It work well. It generate heatmap whith rcolumn clustering dendrogram and I
can export a very nice graph. But I don not know how
2006 Mar 06
2
Problems with heatmap.2 in the gregmisc package
Hi
Sorry to revisit an old problem, I seemed to solve this in 2004, only
for it to resurface :-S
I am trying to plot a heatmap, and I don't want the columns of my matrix
re-ordered. The function doesn't seem to behave as the help would have
you believe:
a <- matrix(rnorm(100),nr=20)
a.d <- dist(a)
a.hc <- hclust(a.d)
a.de <- as.dendrogram(a.hc)
# columns are re-ordered
2005 Jun 27
0
row-side color bars do not reverse properly in heatmap (PR#7972)
Full_Name: Kevin R. Coombes
Version: 2.1.0
OS: Windows XP
Submission from: (NULL) (143.111.224.169)
When revC = TRUE and RowSideColors is set to a list of colors in heatmap, then
the image and dendrogram are inverted, but the row-side color map does not
change. The following script illustrates the problem.
##############
set.seed(1023)
# generate columns of two different types
d1 <-
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 =
2004 Oct 20
0
heatmap.2 ordering & color key
HI All
sorry if this question has already been asked but I couldn't find
anything that answered my question
I have 24 columns of data that I'm trying to plot in heatmap.2
(gregmisc) and I'm having difficulty ordering them except in numerical
sequence:
I have transposed my matrix so it will appear with the dendrogram I want
appearing at the top of the heatmap
If I use either of