Displaying 20 results from an estimated 10000 matches similar to: "How to re-order clusters of hclust output?"
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
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
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
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 Jun 17
1
Re: Clustering in R
Thanks a lot, Michael!
I cc to R-help, where this question really belongs {as the
'Subject' suggests itself...} -- please drop 'bioconductor' from
CC'ing further replies.
>>>>> "michael" == michael watson (IAH-C) <michael.watson at bbsrc.ac.uk>
>>>>> on Thu, 17 Jun 2004 09:16:59 +0100 writes:
michael> OK, admittedly it
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
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
2008 May 16
2
heatmap on pre-established hclust output?
Hi,
Can someone please guide me towards how to produce "heatmap" output from the
output of "hclust" run prior to the actual "heatmap" call? I have some
rather lengthy clustering going on and tweeking the visual output
with "heatmap" recalculating the clustering every time is not feasible.
Thanks, Joh
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
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 May 10
3
Colouring hclust() trees
I have a data set with 6 variables and 251 cases.
The people who supplied me with this data set believe that it falls
naturally into three groups, and have given me a rule for determining
group number from these 6 variables.
If I do
scaled.stuff <- scale(stuff, TRUE, c(...the design ranges...))
stuff.dist <- dist(scaled.stuff)
stuff.hc <- hclust(stuff.dist)
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>
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")
2010 Sep 08
1
saving heatmaps in graphical format that can be edited in graphic editor tool
I generated a heatmap in R using the following commands:
> mydata <- read.csv(file="Data.csv", header=TRUE, sep=",")
> mydata <- mydata[rowSums(mydata[,-1]^2) >0, ]
> rownames(mydata)=mydata$Name
> mydata <- mydata[,2:253]
> mydatamatrix <- data.matrix(mydata)
> mydatascale <- t(scale(t(mydatamatrix)))
> hr <-
2010 Sep 17
1
Question: how to obtain the clusters of genes (basically the ones in the row dendrograms) from an object obtained by heatmap.2 function
Hello R-Helpers,
I have a question about extracting the clusters of genes after we make the
heatmap (say ht4) using the heatmap.2 function. Basically, I want to get the
clusters which are shown as row dendrogram in the heatmap.
I understand that ht4$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
2010 Sep 08
2
saving heatmaps in graphical format that can be edited in graphic editor tools
I generated a heatmap in R using the following commands:
> mydata <- read.csv(file="Data.csv", header=TRUE, sep=",")
> mydata <- mydata[rowSums(mydata[,-1]^2) >0, ]
> rownames(mydata)=mydata$Name
> mydata <- mydata[,2:253]
> mydatamatrix <- data.matrix(mydata)
> mydatascale <- t(scale(t(mydatamatrix)))
> hr <-
2003 Oct 17
1
heatmap function
Hi all,
By default, the heatmap function gives an image with a dendrogram added
to the
left side and to the top. Is it possible to only add the dendrogram to
the left side
and let the order of the columns unchanged ?
I tried
heatmap(mat, col=rbg,Rowv=res.hclust$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
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,
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
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)