Displaying 20 results from an estimated 30000 matches similar to: "Changing label size in plot.dendrogram"
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 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
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
2007 Jun 13
2
Formatted Data File Question for Clustering -Quickie Project
I am trying to learn how to format Ascii data files for scan or read
into R.
Precisely for a quickie project, I found some code (at end of this
email) to do exactly what I need:
To cluster and graph a dendrogram from package (stats).
I am stuck on how to format a text file to run the script.
I looked at the dataset USArrests (which would be replaced by my data
and labels) using UltraEdit. That
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 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
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)
2005 Jul 11
1
indexing into and modifying dendrograms
I would like to be able to exert certain types of control over the
plotting of dendrograms (representing hierarchical clusterings) that I
think is best achieved by modifying the dendrogram object
prior to plotting. I am using the "dendrogram" class and associated
methods.
Define the cluster number of each cluster formed as the corresponding
row of the merge object. So, if you are
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
2010 Apr 13
0
Coloring leaves in Dendrogram according to gene names
Hello,
I am a new R user and have a question regarding dendrogram coloring.
I would like to color each leaf in the dendrogram (dhc) according to a
specific criterion. For me this criterion is the gene name.
For this, I created a data.frame with 2 variables: The gene name and the
corresponding color.
Using the following function, adapted from "dendrapply {stats}", I still
have the same
2004 May 06
1
question about plot.dendrogram
hi all,
i'm trying to plot a dendrogram with labeled leaves
>rownames(f)<-v.names
>v<-rowMeans(f, na.rm=T)
>clust<-hclust(dist(v))
>dend<-as.dendrogram(clust,hang=0.05)
>clust2<-cut(dend, h=0.5)
>class(clust2$low[[1]])
>[1] "dendrogram"
then
>plot(clust2$low[[1]],horiz=TRUE,frame=F,type = "tr"))
but my leaf labels do not fit
2008 May 06
1
Dendrogram label size
Is it possible to resize the labels in a dendrogram without applying
circles and triangles to edges?
I tried cex.labels:
plot(scoreDendogramObj, horiz=TRUE, axes=FALSE, cex.labels=0.8)
but that didn't have any effect.
Thanks,
Alex
2012 Oct 24
0
recursive function on a structured list of lists (dendrogram)
Dear all,
I have been trying the following without avail and would be very grateful for any help. From a dendrogram (recursive list of lists with some structure), I would like to obtain some information of the component lists and of the enclosing list at the same time. In dendrogram-speech I basically would like the label of the leaf and the height of the enclosing branch.
A dendrogram example
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 Jun 28
0
neatmap - draw.dendrogram - help!
Hi all,
I'm having a problem where by I'm trying to use the NeatMap draw.dendrogram
function as it is more versatile in placement/direction of dendrograms,
instead of the limited plot function.
Using plot I can get my dendrograms to display the species name for each
leaf of the tree. But I cannot figure out how to make this happen using
draw.dendrogram..
genetic<-
2007 Mar 09
1
dendrogram - got it , just need to label :)
Hi all, Hi Gavin,
thx for your help i finally found out what i want to do and how to
fix it.
just needed to get some more level my cut level was too small...
two question remain...
a) can i somehow scale the twigs after cutting ?
b) how can i label the nodes and how to label which one...
thx !!
-m.
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$upper)
--[dendrogram w/ 2 branches and 4 members at h = 152]
|--[dendrogram w/ 2 branches and 2 members at h = 77.6]
| |--leaf "Branch 1" (h=
2011 Sep 26
0
horizontal labels for a dendrogram
Dear R-help list,
I'd like to create visualize the clustering of a dataset with a
dendrogram. I'm using the following script:
data = read.table("data.csv", header=T, sep=";")
require(cluster)
res = as.dendrogram(agnes(data))
chlab <- function(n) {
if(is.leaf(n)) {
att <- attributes(n)
labx <- data$category1[att$label]
lab_color <- ifelse(labx ==
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
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