Displaying 20 results from an estimated 3000 matches similar to: "question about plot.dendrogram"
2015 May 18
2
A "bug" in plot.dendrogram - can't plot lty with character color
The problem:
===========
Once a dendrogram has a branch with both a line type AND a color (which is
a character color), the plot.dendrogram function will not plot and return
an error.
I say this is a bug because (I believe), we would like a dendrogram to be
able to use character colors, while also allowing control over line types.
This e-mail includes an example, and what I think a solution
2007 Nov 25
2
accessing the "address" of items in a recursive list
Dear useRs,
I am working on a project involving the clustering of a large dataset. I need to extract specific sub-clusters from the parent dendrogram for further analysis. The data is too large for the use of convenient tools such as identify.clust (it selects the specific group of interest on a graph), so alternatively I have saved the plot as a large image file so that it can be printed or
2004 Jul 19
1
Dendrogram plotting options?
Hi, I was wondering if there is more flexibility in the output of
dendrograms when plotting a hclust object. I can't seem to find
information on how to change the default output of a "hanging" style
tree with the axis on the right to a left-to-right plot with and axis
on the bottom. Example code follows:
library(vegan) #loads the "vegan" module that compuptes ANOSIM
2005 Nov 02
1
x/y coordinates of dendrogram branches
Dear R-users,
I need some help concerning the plotting of dendrograms for hierarchical
agglomerative clustering.
The agglomeration niveau of each step should be displayed at the
branches of the dendrogram.
For this I need the x/y coordinates of the branch-agglomerations of the
dendrogram.
The y-values are known (the heights of the agglomeration), but how can I
get the x-values?
> mydata
2008 Feb 04
1
Concatenation and Evaluation
Hello all,
I've run into what I bet is a silly problem; however, I've been
trying to get around it now for a couple weeks and every time I think
I have the answer it still doesn't work. So I apologize in advance
if this is painfully obvious, but I've run out of ideas and would
really appreciate any input.
My situation is this, I'm importing a number of tab
2005 Oct 23
1
Coloring leaves, twigs and labels in plot.dendrogram()
Core developers,
I couldn't find any simple way to send a vector of colors to apply to each
terminal in plot.dendrogram() or plot.hclust()---I asked R-help about it a
few weeks ago and didn't get any response---so I hacked that functionality
into the plot.dendrgram code (see below for hacked function plus
examples)....
Is there any chance this functionality could be added to 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
2010 Jun 17
1
plotting radial dendrograms
Dear list,
I am trying to plot a radial dendrogram using the ape package, which
requires my data to be of class 'phylo'. Currently I have my
dendrogram stored as an object of class 'dendrogram' which was
produced from an outside bit of C code, but was made into an object of
class 'igraph.eigenc' and converted to a dendrogram using
'as.dendrogram()' from the igraph
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
2011 Sep 13
2
help with hclust and cutree
Hello,
I would like to cut a hclust tree into several groups at a specific
similarity. I assume this can be achieved by specifying the "h" argument
with the specified similarity, e.g.:
clust<-hclust(dist,"average")
cut<-cutree(clust,h=0.65)
Now, I would like to draw rectangles around the branches of the
dendrogram highlighting the corresponding clusters, as is done by
2005 May 18
0
dendrogram and dendrapply
Hi all,
I think I have some problems to use correctly the function dendrapply.
Let suppose dend is a dendrogram object.
I would likde to know the cardinal number of leaves depending of each
node of the tree dend.
It is right that the command attr(dend,"members") gives the total number
of leaves, and
attr(dend[[1]],"members") gives the number of leaves for the first left
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
2010 Nov 15
1
plot.dendrogram() plot margins
Hello,
Is it possible to remove those extra margins on the "sample" axis from
plot.dendrogram:
par(oma=c(0,0,0,0),mar=c(0,0,0,0))
ddr<-as.dendrogram(hclust(dist(matrix(sample(1:1000,200),nrow=100))))
stats:::plot.dendrogram(ddr,horiz=F,axes=F,yaxs="i",leaflab="none")
vs.
stats:::plot.dendrogram(ddr,horiz=T,axes=F,yaxs="i",leaflab="none")
2009 Jul 21
1
problem with heatmap.2 in package gplots generating non-finite breaks
I have written a wrapper for heatmap.2 called
heatmap.w.row.and.col.clust which auto-generates breaks using
breaks<-round((c(seq(from=(-20 * stddev), to=(20 * stddev))))/20,
digits = 2) #(stddev in this case = 2.5)
This has always worked well in the past but now I am getting an error
that non-finite breaks are being generated. Drilling down, it seems
that my wrapper is generating finite
2009 Jun 19
1
Drawing dendrogram
Dear all,
I would like to draw a dendrogram and mark some parts/branches (by using "segments") including their labels. If I draw it without specifying the length of x axix, I am able to do that (as in My dendrogram 1 of the following codes). However, if I want to specify the x axix, I am not able to draw marking line (by using "segments") including labels (as in My dendrogram
2003 Jul 17
2
i need help in cluster analyse
Hello,
My name is Rodrigo, I am using R program and I have a trouble.
I am trying to do a dendrogram with genetics information.
Let me explain...
The Similarity Matrix was already did, and with this matrix I want to construct a dendrogram.
So, the distance is done. I need to transform this matrix (that I have) in a dendrogram,
I woud be very grateful if someone could help me.
PS: I am sending
2002 Jan 13
1
changing the ordering of leaves in a dendrogram
I'd like to change the way plot.hclust displays an hclust object. Here's
a description of how it's done now, from the R documentation of hclust:
In hierarchical cluster displays, a decision is needed at each merge
to specify which subtree should go on the left and which on the right.
Since, for n observations there are n-1 merges, there are 2^{(n-1)}
possible
2015 May 20
0
Probably a "bug" in the dendextend package
>>>>> Tal Galili <tal.galili at gmail.com>
>>>>> on Mon, 18 May 2015 23:01:44 +0300 writes:
> The problem:
> ===========
> Once a dendrogram has a branch with both a line type AND a color (which is
> a character color), the plot.dendrogram function will not plot and return
> an error.
If the dendrogram has been messed up
2008 Jul 24
1
plot.dendrogram xlim/ylim
list(...),
I would like to zoom in to the leaves of large trees in a dendrogram
plot. The playwith package allows zooming by passing xlim and ylim
arguments to the plot call (Hmisc does this too I think). But
currently stats:::plot.dendrogram does not accept xlim or ylim. So I
would like to enable that. In place of the existing code chunk:
xlim <- c(x1 - 1/2, x2 + 1/2)
ylim <- c(0,
2010 Apr 17
2
Interacting with dendrogram plots, locator() or click()
I would like to explore dendrogam plots interactively. For example, click on a node and return information about all of the children of that node.
Is there a high level wrapper for locator() or click() that will return the nearest dendrogram node on a plot?
If not, is there a way to obtain the [x,y] coordinates of all the nodes on a plot?
Thanks,
David
David J. States, M.D., Ph.D.
Professor