Displaying 20 results from an estimated 6000 matches similar to: "dendrogram again"
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
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:
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
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 <-
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
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 Jan 12
3
Problems creating a PNG file for a dendrogram: "Error in plot.window(...) : need finite 'xlim' values"
Has anyone successfully created a PNG file for a dendrogram?
I am able to successfully launch and view a dendrogram in Quartz. However, the dendrogram is quite large (too large to read on a computer screen), so I am trying to save it to a file (1000x4000 pixels) for viewing in other apps. However, whenever I try to initiate a PNG device, I get a "need finitite 'xlim' values"
2005 Dec 16
2
dendrogram branches with different lty
Dear r-list,
I am trying to visually seperate the two main clusters of a dendrogram.
The idea is to use:
'edgePar=list(lty=3)' for 'dend1[[1]]' and
'edgePar=list(lty=1)' for 'dend1[[2]]'
I have not found a way to solve this. Any suggestions?
Patrick
hc <- hclust(dist(USArrests), "ave")
(dend1 <- as.dendrogram(hc))
par(mfrow=c(2,2))
plot(dend1)
2008 Jun 02
1
Plotting horizontal dendrograms
I am using hclust and plot to produce dendrograms. Using my input data I am
able to complete an analysis and obtain a vertical plot.
I want to be able to plot the dendrogram horizontally.I am using version 2.6
of R and have updated my packages recently.
Using the sample script for dendrograms I can produce a horizontal plot
using the instruction horiz = TRUE in plot().
When I use the same
2007 Oct 26
2
cut.dendrogram and cutree
Hi!
In the example:
hc <- hclust(dist(USArrests), "ave")
dend1 <- as.dendrogram(hc)
dend2 <- cut(dend1, h=70)
Do the branches "Branch 1", "Branch 2", "Branch 2"...in dend2$upper
str(dend2$upper)
--[dendrogram w/ 2 branches and 4 members at h = 152]
|--[dendrogram w/ 2 branches and 2 members at h = 77.6]
| |--leaf "Branch 1" (h=
2002 Mar 05
1
no labels when plotting dendrograms
I'd like to be able to cut dendrograms at a height I specify
and then plot the resulting subtrees. I wanted to use the
dendrogram object for this purpose because there doesn't seem
to be a canned way to cut a hclust object and get a list of
hclust objects, but there is a function (cut) that does that
for dendrograms. The problem I'm having is that when I plot
a dendrogram, I
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
2004 Sep 08
1
plot.dendrogram
Dear R-users,
I would like to change the labels size and format in the node ends of a dendrogram, how can I do it?
How can I use different symbols/colors in each node ends ?
I manage to do it with plot.cluster, but heat map uses plot.dendrogram.
Can anyone help me please?
thank you
Marta
[[alternative HTML version deleted]]
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
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 Dec 09
1
how to add an edgetext to a dendrogram?
Hello to all,
I'd like to colour the different labels of my dendrogram. How can I do? I
guess I could to 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")
plot(dend1)
labels (USArrests) [[1]] # to know how many cities
2003 Sep 24
5
splitting clusters
Hi All:
I am clustering 500 genes using hclust of R. Visualizing cluster
membership becomes difficult with so many genes in each cluster...Is there
a way of printing the dendrogram in multiple pages so that I can clearly
see what is in each cluster?
Thanks in advance.
Karthi.
2018 May 08
2
Pruning a dendrogram based on frequencies
How can one prune a dendrogram (plot.dendrite, plotrix) based on a minimum level of frequencies?. Franklin.?
[[alternative HTML version deleted]]
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)
2007 Mar 09
1
how can i group branches of a dendrogram
Hi all,
how can i group branches of a dendrogram ?
thx in advance