Displaying 20 results from an estimated 9000 matches similar to: "node stack overflow when extracting labels from a dendrogram"
2006 Jan 27
1
Justification of dendrogram labels
Hi all,
Can someone tell me how to justify (right or left) the labels on the
branches of a dendrogram tree? I have produced a dendrogram via agnes and
plotted it with pltree. The dendrogram terminal branch labels seem to be
centre-justified by default and I was hoping to change this to left
justification. Thanks,
Duncan
*****************************************
Dr. Duncan Mackay
School of
2008 Nov 21
2
Dendrogram labels
Is there any way to change the orientation of the labels on the end of the dendrograms to horizontal rather than vertical? If so, how can I do that.
_____________________________________________
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute - Webb Lab
333 Bostwick Avenue NE
Grand Rapids, MI 49503
ph. 616.234.5787
This email message,
2011 Dec 12
1
how to colour labels (each label with a colour) in a dendrogram?
Hello to all,
I still have this doubt.
I'd like to colour the different labels of my dendrogram each one with a
different colour. How can I do? I guess I could do using *edgetext* and
then *t.col* or* lab.col* but I don't know how to add edgetext to my
dendrogram. Can you help me please?
Example:
require(graphics); require(utils)
hc <- hclust(dist(USArrests), "ave")
(dend1
2010 Mar 11
2
cluster analysis labels for dendrogram
Hi,
I am clustering data based on three numeric variables. I have a fourth
variable that is categorical (site) which I would like to use to label the
leaves of my dendrogram, so I can see how the different sites are grouped
throughout the tree, but I do NOT want to use this variable in the cluster
analysis itself. Is there any way I can do this?
Thanks,
Samantha
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2007 Jul 23
1
change text labels on a dendrogram
Hi all:
I already made a dendrogram, I want to change the labels; In my data set
there is one column with text that I want to set as the labels, any one can
tellme how can I do it?
Thanks,
Ana Marcela
[[alternative HTML version deleted]]
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
2011 Jan 25
1
dendrogram plot does not draw long labels ?
Hello,
It seems that the plot function for dendrograms does not draw labels when
they are too long.
> hc <- hclust(dist(USArrests), "ave")
> dend1 <- as.dendrogram(hc)
> dend2 <- cut(dend1, h=70)
> dd <- dend2$lower[[1]]
> plot(dd) # first label is drawn
> attr(dd[[1]], "label") <- "aaaaaaaaaaaaaaaaaa"
> plot(dd) # first label is
2006 Sep 15
1
what does Height represent?
hi--
I am new to R and try to use R cluster my binary data. I use
hierarchical clustering
plot (hclust (dist(x,method="binary"),method="average"),cex=0.1)
I end up with a cluster Dendrogram. On the left of my dendrogram, there
is scale called Height from 0.0 to 1.0.
I don't understand what does Height represent. If the Height represents
the distance scale between two
2007 Mar 09
1
dendrogram again
Hi all,
ok, i know i can cut a dendrogram, which i did.
all i get is three objects that a dendrograms itself.
for example:
myd$upper, myd$lower[[1]], myd$lower[[2]]
and so on. of course i can plot them seperately now.
but the lower parts still have hundreds of branches. i?ll need a 30 "
widescreen to watch the whole picture.
what i?d like to is group the lower branches , so that i get a
2007 Mar 09
1
dendrogram / clusteranalysis plotting
Dear all,
i performed a clusteranalysis - which worked so far...
i plotted the dendrogram and sooo many branches, a rough sketch would
be enough ;)
i tried max.levels therefore which worked, but not for the plot...
i used the following
plot(hcd,nodePar =nP, str(hcd,max.level=1))
the output on the terminal was:
--[dendrogram w/ 2 branches and 196 members at h = 2.70]
|--[dendrogram w/ 2
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
2017 Mar 23
1
A question on stats::as.hclust.dendrogram
Hi all,
This is the first time I'm writing to R-devel, and this time I'm just asking for the purpose for a certain line of code in stats::as.hclust.dendrogram, which comes up as I'm trying to fix dendextend.
The line in question is at line 128 of dendrogram.R in R-3.3.3, at stats::as.hclust.dendrogram:
stopifnot(length(s) == 2L, all( vapply(s, is.integer, NA) ))
Is there any
2006 Feb 28
1
creating dendrogram from cluster hierarchy
Dear R users,
I have created data for hierarchical agglomerative cluster analysis
which consist of the merging pairs and the agglomeration heights, e.g.
something like
my.merge <- matrix(c(-1,-2,-3,1), ncol=2, byrow=TRUE)
my.height <- c(0.5, 1)
I'd like to plot a corresponding dendrogram but I don't know how to
convert my data to achieve this.
Is it possible to create a
2012 Apr 30
2
Generate Dendrogram
Hi
I have a distance matrix which is computed by user defined method. I
would like to plot the dendrogram. I would like to use different color
and want the leaves laying down bottom.
The script like this. I am not familiar with R. I followed the example
shown in
http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dendrogram.html
dist.obj <- as.dist(matrix.distance)
hc.obj <-
2005 Oct 26
1
Dendrogram for many cases
Dear All,
I have a cluster object based on a
dissimilarity matrix from about 1,100
cases and wish to know whether anyone
can think of any tips to display some
form of graphical output which would
give some sense of the similarity
between the cases.
A standard form of dendrogram would be
fine, but with so many cases the
dendrogram on the standard devices
(R-2.20 on NT4) is very compact
2009 Jan 17
1
Dendrogram with the UPGMA method
Hi,
I am clustering objects using the agnes() function and the UPGMA
clustering method (function = "average"). Everything works well, but
apparently something is wrong with the dendrogram. For example:
x<-c(102,102.1,112.5,113,100.3,108.2,101.1,104,105.5,106.3)
y<-c(110,111,110.2,112.1,119.5,122.1,102,112,112.5,115)
xy<-cbind(x,y)
library(cluster)
UPGMA.orig<-agnes(x)
2013 Jan 16
1
dendrogram stops!
Dear I am using the 'as.dendrogram' function from the 'stats' library to convert from an hclust object to a dendrogram with a dataset of size
~30000 (an example code is below). I need the dendrogram structure to
use the "dendrapply" and "attributes" functions and to access the child
nodes, I do not need any of the plot properties.
The problem is that it
2016 Apr 21
2
"cophenetic" function for objects of class "dendrogram"
Hello,
I have been using the "cophenetic" function for objects of class "dendrogram" and I have realised that it gives different results when it is used with objects of class "hclust". For instance, running the first example in the help file of the "cophenetic" function,
d1 <- dist(USArrests)
hc <- hclust(d1, "ave")
d2 <-
2003 Sep 26
1
a. crossing branches with hclust, b. plot.dendrogram
Hello,
a. when I use hclust with the methods media, centroid, and mcquitty,
and plot the results, the dendrograms have lines that are crossing each
other. Is this ok?
b. My next question refers to plot.dendrogram: How can I use parameters
as "hang" or "cex" here? E.g. for
st <- as.dendrogram(subtreeshc[[x]])
I would like to have something like this, where cex and hang
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")