Displaying 20 results from an estimated 3000 matches similar to: "heatmap for gene clustering?"
2004 Apr 23
1
(no subject)
Dear all:
I am developing a package in R. While I am running R CMD check, I found
the following warning message:
Found the following C sources/headers with CRLF line endings:
src/hem.c
src/random4f.h
ISO C requires LF line endings.
It seems that it comes from a line ending problem in C. What are CRLF/LF
line endings?
How can I fix it? Thank you for your help in advance.
Best,
HJ
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
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
2013 Aug 22
1
Interpreting the result of 'cutree' from hclust/heatmap.2
I have the following code that perform hiearchical clustering and plot
them in heatmap.
__
library(gplots)
set.seed(538)
# generate data
y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""),
paste("t", 1:5, sep="")))
# the actual data is much larger that the above
# perform hiearchical clustering and plot heatmap
test <- heatmap.2(y)
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
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
2011 Jul 01
1
highlighting clusters in a heatmap
I would like to draw horizontal or vertical lines on a heatmap to
highlight the clusters at some specified cut depth of the dendrogram.
As a hacked example, the following code would work if I could set the
coordinates of the top and bottom of the false color image correctly
(ymin and ymax), but the correct values seem to depend on the output
device and its size. I realize that heatmaps use a 2x2
2008 Dec 22
3
row sum question
Dear helpers,
I'm using R version 2.8.0.
Suppose that I have a small data set like below.
[,1] [,2] [,3] [,4]
a 1 1 0 0
b 0 1 1 0
c 1 1 1 0
d 0 1 1 1
First, I'd like to find row sum of values uniquely present in each row, but
only sequentially from the top row, meaning that if the value is shown in
the above row(s) already, the
2011 Feb 09
2
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 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 clustered in that way, I have a new order of these genes, and want the
rows of the heatmap are drawed as the order I give. Could anybody help me
on that? Thank you!
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
2009 Jul 23
0
using k-means clustering in conjunction with heatmap.2 function
Hello,
I am trying to create a heatmap that clusters based on a k-means scheme
rather than a hierarchical clustering scheme.
Suppose I have the following input data, located in sample.table:
x1 x2 x3 x4
x1 17.198 16.306 16.806 16.374
x2 14.554 10.866 15.780 14.596
x3 14.374 14.118 14.569 17.352
x4 17.505 14.596 15.738 14.070
By using the heatmap.2 function as follows, I can create a heatmap
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 =
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
2002 Jul 19
2
Plotting a section of a dendrogram
> I have performed clustering analysis with hclust (Ward's method) on a
> database of 800 samples. As you may imagine the full dendrogram is not
> really readable. I have obtained groups with cutree. I would like to
plot
> sub-sections of my big dendrogram to show group 1, group 2 and so on.
I don't think R has anything like subtree in Splus, unfortunately. I
think what has
2011 Jul 24
0
setting distance matrix and clustering methods in heatmap.2
heatmap.2 defaults to dist for calculating the distance matrix and hclust for
clustering.
Does anyone now how I can set dist to use the euclidean method and hclust to
use the centroid method?
I provided a compilable sample code bellow.
I tried: distfun = dist(method = "euclidean"),
but that doesn't work. Any ideas?
library("gplots")
library("RColorBrewer")
test
2013 May 21
1
keep the centre fixed in K-means clustering
Dear R users
I have the matrix of the centres of some clusters, e.g. 20 clusters each
with 100 dimentions, so this matrix contains 20 rows * 100 columns numeric
values.
I have collected new data (each with 100 numeric values) and would like to
keep the above 20 centres fixed/'unmoved' whilst just see how my new data
fit in this grouping system, e.g. if the data is close to cluster 1
2010 Aug 09
1
Need help on heatmap, K-means and hhierarchical clustering methods
Hi folks,
I am new to the R software. I have been going through different materials to
know more about R.
I have the R software installed on my windows machine.I would like to know
the R source code for the following problems on iris flower data set.
I need to do the cluster analysis project with the iris data set. The goal
is to cluster the flowers
according to their Sepal.Length, Sepal.Width,
2008 Sep 09
3
Splitting Data Frame into Two Based on Source Array
Dear all,
Suppose I have this data frame:
> data_main
V1 V2
foo 13.1
bar 12.0
qux 10.4
cho 20.33
pox 8.21
And I want to split the data into two parts
first part are the one contain in the source array:
> src
[1] "bar" "pox"
and the other one the complement.
In the end we hope to get this two dataframes:
> data_child1
V1 V2
bar 13.1
pox
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")
1999 Sep 22
2
SAMBA digest 2240
>
Hi,
Check if the shared directory has the write permission for all. i.e. chmod 777 for
the particular directory
> Date: Sun, 19 Sep 1999 21:06:36 -0700
> From: Kenny Cho <Kenny.Cho@Corp.Sun.COM>
> To: samba@samba.org
> Subject: Problem copying files to samba mount.
> Message-ID: <37E5B2CC.9ADC9F8A@ha1pal.corp.sun.com>
> MIME-Version: 1.0
>