Displaying 20 results from an estimated 10000 matches similar to: "Problem with duplicates in row.names"
2012 Sep 09
3
how to save a heatmap.2 in png /jpeg /tiff
Hey, I am still working on my heat map (for those who are read my previous post about row.names)…
Now, I would like to save my heat map.2 in .png or .tiff in order being able to work on the picture in photoshop, but it doesn't work.
I'am using (as I have found on some forum)
> png("heatmap.2.png) # and it just doesn't work. when I try doing it with::
2018 Mar 01
3
how to make row.names based on column1 with duplicated values
Dear All,
Suppose I have a dataframe like this with many thousands rows all with
different names:
data.frame(gene=c("a","b","c","d","c","d","c","f"),value=c(20,300,48,55,9,2,100,200)),
I want to set column "gene" as row.names, but there are duplicates (c, d),
which I want to transform into this as row names:
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!
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
2005 Jun 16
2
heatmap aspect ratio
Hi all,
Does anyone know of a fairly easy way to "stretch" a heatmap
vertically? I've got 42 arrays and would like to be able to see as
many significant genes as possible (right now I can only get 50 genes
with it still being readable). In some comparisons there are several
hundred significant genes.
I've fiddled with the "asp" argument, but that doesn't
2009 Nov 17
2
question about function heatmap
Hi,
I am using the function heatmap(stats) to draw a microarray heatmap,
columns are samples and rows are gene features.
I did a 2D clustering during the heatmap drawing. The features and
samples indeed cluster into several blocks both vertically and
horizontally.
I can get the index of re-ordered rows and columns after the heatmap
drawing by typing the the return variable of the heatmap
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,
2018 Mar 01
0
how to make row.names based on column1 with duplicated values
On Wed, 28 Feb 2018, Stephen HonKit Wong wrote:
> Dear All,
> Suppose I have a dataframe like this with many thousands rows all with
> different names:
> data.frame(gene=c("a","b","c","d","c","d","c","f"),value=c(20,300,48,55,9,2,100,200)),
>
> I want to set column "gene" as row.names, but
2004 May 05
1
heatmap for gene clustering?
I am using "heatmap" to cluster genes in microarrays. It works fine with
100~200 genes.
But when I draw a heatmap with 600 genes, I can't read a clustering tree
well.
Maybe I will be able to read it by dividing it into several subtrees using a
function such as "subtree".
I found "subtree" in Splus, but not in R. Is there a similar function in R?
Or, without it,
2011 Jan 20
1
Question on RData and Rhistory extentions
Hi,
It seems simple but I could not find the solution on the R site.
I can't save properly ".RData" and ".Rhistory" in Windows 7 folders. I get
files with no extension.
Thanks in advance for your help.
JP
Jean-Philippe Puyravaud
9A Frederic Osanam Street
Colas Nagar
Puducherry 605001
E-mail: <mailto:jp.puyravaud@gmail.com>
2011 Nov 08
3
ggplot2 reorder factors for faceting
Dear List
I am trying to draw a heatmap using ggplot2. In this heatmap I have faceted my data by 'infection' of which I have four. These four infections break down into two types and I would like to reorder the 'infection' column of my data to reflect this.
Toy example below:
library(ggplot2)
# test data for ggplot reordering
genes <- (rep (c(rep('a',4),
2008 Mar 05
2
t.test & p-Value
Hello list,
I am trying to apply the paired t.test between diseased and not diseased
patients to identify genes that are more expressed in the one situation
under the other. In order to retrieve the genes that are more expressed in
the positive disease state I do:
p.values<-c()
for(i in 1:length(Significant[,1])){
p.values[i]<-try(t.test(positive[i,],negative[i,],alternative
2011 Jan 05
1
Heat map in R
Hello,
I am trying to make a heatmap in R and am having some trouble. I am very new
to the world of R, but have been told that what I am trying to do should be
possible. I want to make a heat map that looks like a gene expression
heatmap (see http://en.wikipedia.org/wiki/Heat_map).
I have 43 samples and 900 genes (yes I know this will be a huge map). I also
have copy numbers associated with
2010 Sep 18
1
Drawing Heatmap using gplots
Hi,
I am using heatmap.2 of gplots to make heatmaps of my the attached file. I
am giving my code for the same ..
library(gplots)
x=read.table("1.txt", header=TRUE)
mat=data.matrix(x)
heatmap.2(mat, col=greenred(75),
Rowv=TRUE,
Colv=TRUE,
distfun = dist,
hclustfun = hclust,
dendrogram = c("both"),
scale = c("row"),
na.rm=TRUE,
trace="none",
2013 Apr 21
1
cluster gene list
Hi,
I have created a heatmap using heatmap.2 having 7 clusters. I would like
to extract the list of genes that are in these 7 clusters.
Is there any function that can be used to extract genes for each cluster?
Cheers,
Sudhir
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2010 Mar 29
1
stuck with affy / limma
Hi,
I have a question concerning the analysis of some affymetrix chips. I
downloaded some of the data from GEO GSE11324 (see below). In doing so I'm
stuck after I identified the probesets with significant changes. I have
problems in assigning probeset specific gene names as well as getting the
genomic coordinates. Furthermore I have no clue how to deal with the fact,
that most genes have
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
2013 Mar 12
1
Request for more flexibility in heatmap() width / height ratio
Hi R users,
I'm a quite extensive user of the heatmap() function, and as many others
i'm frequently frustrated by its fixed square width / height ratio. Here is
a typical example :
dev.new()
heatmap(matrix(rnorm(1200), nrow=10))
I have a non square matrix to plot with heatmap, as there are many more
columns than rows, row labels are larger than necessary but column labels
2011 Aug 08
1
Creating a simple 1-row heatmap
Howdy,
I am trying to make a simple monochrome heatmap from 1 row of data.
Essentially, I just want a long bar where black represents the max value in
the data, white is the minimum, and all values in between are interpolated
appropriately. I have tried using heatmap and heatmap.2, but both have
issues. heatmap seems to be restricted to only drawing a square plot, and
this data requires a