Displaying 20 results from an estimated 10000 matches similar to: "How to replace the row number for each product by real product name in as.dendrogram in cluster analysis..HELP!"
2005 Dec 12
1
dendrogram: how to obtain leaf height
Dear All,
How can the height of a leaf be extracted from a dendrogram?
Sure, I can print it, but I am not able to, say, store it in an object. I think I understand that the height is a property of the split, not the leaf itself, but the printing functions display a "height" or "h" (which changes with "hang") and that is what I want. Obviously, the info is there
2012 Aug 12
0
Different cluster orderings from cutree() and cut.dendrogram()
Hi!
I just discovered that cutree() and cut.dendrogram() do not assign the
same cluster numberings when called on the same tree. More specifically,
cutree() assigns cluster numbers by order of appearance in the data,
while cut.dendrogram() sorts clusters by height (see example below). I
guess this is for historical reasons?
I'm hit by this difference when I want to get a vector of cluster
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
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
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
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
2016 Apr 21
1
"cophenetic" function for objects of class "dendrogram"
Note that cophenetic.default (which works on the output of hclust(dist(X)))
uses the
row names of X as labels. as.dendrogram.hclust does not retain those row
names
so cophenetic.dendrogram cannot use them (so it orders them based on the
topology of the dendrogram).
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Thu, Apr 21, 2016 at 7:59 AM, William Dunlap <wdunlap at tibco.com> wrote:
2009 Apr 03
0
dendrogram rect.hclust() not working?
I have tried to use rect.hclust() to draw a rectangle around a set of
leaves, but am running into trouble.
The rect.hclust() is drawing two rects instead of one, and of the
wrong size:
--------------------
scoreClusterObj <- hclust(scoreDistanceObj, method=clustMethod)
order <- scoreClusterObj$order
orderedLabels <- rep(0, length(order))
for (orderIndex in 1:length(order)) {
# this
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
2008 Aug 01
0
hclust interrogation & use of $merge for dendrogram annotation?
Hi all,
I've been doing some investigation to see if it is possible to implement an hclust/dendrogram related requirement that I've been given. So far ?hclust and a lot of googling haven't provided the information I'm looking for (I've been using R sporadically for a year).
The requirement I have is to:
On a dendrogram plot, draw points at various merge locations, based on
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 <-
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
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 <-
2011 Apr 28
1
visualizing bootstrapped dendrogram
I want to classify bipolar neurons in human cochleas and have data of the
following structure:
Vol_Nuc Vol_Soma
1 186.23 731.96
2 204.58 4370.96
3 539.98 7344.86
4 477.71 6939.28
5 421.22 5588.53
6 276.61 1017.05
7 392.28 6392.32
8 424.43 6190.13
9 256.41 3850.51
10 249.17 3118.14
11 276.97 3037.29
12 295.30 3703.76
13 314.43 5265.97
14 301.15 5781.73
I
2011 Apr 01
2
hc2Newick is different than th hclust dendrogram
Hi R helpers... I am having troubles because of the discrepancy
between the dendrogram plotted from hclust and what is wrote in the
hc2Newick file. I've got a matrix C:
> hc <- hclust(dist(C))
> plot(hc)
with the:
> write(hc2Newick(hc),file='test.newick')
both things draw completely different "trees"...
I have also tried with the raw distance matrix D and
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
2002 May 14
0
RE: cut.dendrogram (PR#1552)
I'm resending this bug report with a new example. As seen below,
cut.dendrogram gives an error message for some heights, but not for others
and with some datasets adn not others. I can't see why.
Last time I unwittingly sent my message with HTML formatting. This time I'm
travelling and using an e-mail system that I am unfamiliar with. As far as
I can see, I am not using HTML.
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
2016 Apr 21
0
"cophenetic" function for objects of class "dendrogram"
I think the results differ only in the order of the labels. The following
function
puts the labels in a standard order and then the results are the same:
canonicalize.dist <- function (distObject)
{
o <- order(labels(distObject))
as.matrix(distObject)[o, o, drop = FALSE]
}
identical(canonicalize.dist(d2), canonicalize.dist(d3))
[1] TRUE
Bill Dunlap
TIBCO Software
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