Displaying 20 results from an estimated 1000 matches similar to: "Hierarchical clustering using own distance matrices"
2010 May 20
2
Overlap of leaf labels
Hi,
I have tried looking at the archives but havent found any answer that works
till now (Sorry if i have missed anything)
I am a newbie to R and i am trying to carry out hierarchical clustering
using hclust -> as.dendrogram and then plotting the results as a dendrogram
using the plot function plot(object).
My question is :
In the function "plot", can one decrease the leaf label
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 <-
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
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
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
2005 Dec 01
1
R Hierarchical clustering leaf node
Hello,
I am new to the R package. After I use R to perform the hierarchical
clustering, I am only interested in retrieving the leaf nodes that share
the last common ancestors. As illustrated below, I'd like to retrieve (B,
C) as a cluster and then (D, E) as another cluster. Any chance to do
this in R? Thanks! BTW, I just subscribed to this list (not sure if the
subscription is
2008 Mar 08
1
Elbow criterion plots for determining k in hierarchical clustering
Hi There,
I'm working on some cluster analyses on a large data-set using hclust with
Wards method and Manhattan (city block) distance measures. I've created
dendrograms to illustrate the clustering criteria, but would like to create
a plot to examine for the classic elbow criterion to use in determining the
best number of clusters. Ideally I'd like to plot percent variance
explained
2008 Feb 11
1
Dendrogram for agglomerative hierarchical clustering result
Hey group,
I have a problem of drawing dendrogram as the result of my program
written in C. My algorithm is a approximation algorithm for single
linkage method. AS a result I will get the following data:
[Average distance] [cluster A] [cluster B]
For example:
42.593141 1 26
42.593141 4 6
42.593141 123 124
42.593141 4 113
74.244206 1 123
74.244206 4 133
74.244206 1 36
So far I have used C to
2012 Feb 23
2
Advice on exploration of sub-clusters in hierarchical dendrogram
Dear R user,
I am a biochemist/bioinformatician, at the moment working on protein
clusterings by conformation similarity.
I only started seriously working with R about a couple of months ago.
I have been able so far to read my way through tutorials and set-up my
hierarchical clusterings. My problem is that I cannot find a way to obtain
information on the rooting of specific nodes, i.e. of
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
2010 Feb 21
1
How to: Compare Two dendrograms (Hierarchical Clusterings) ?
Hello all,
I wish to compare two dendrograms (representing Hierarchical Clusterings).
My problems are several:
1) how do I manually create a dendrogram object ?
That is, how can I reconstruct it as an "hclust" object that creates such a
dendrogram, when all I have is the dendrogram image (but don't have the
underlaying distance matrix that produced it) ?
I see that there is a
2008 Apr 27
1
An ANOVA test that uses a distance matrix like hierarchical cluster analysis?
Hi All,
I have a question which does not pertain directly to the use of R but comes
from my use of R!
I have data which can be described as 3-dimensional e.g. (x,y,z), with no
negative component. The suggested way to analyze this data is via
multivariate techniques or by calculating what amounts to a levene's test on
the data and then an ANOVA on the three components if the first test is
2012 Mar 08
2
hierarchical clustering of large dataset
Hello All,
i've a set of observations that is in the form :
a, b, c, d, e, f
67.12, 4.28, 1.7825, 30, 3, 16001
67.12, 4.28, 1.7825, 30, 3, 16001
66.57, 4.28, 1.355, 30, 3, 16001
66.2, 4.28, 1.3459, 13, 3, 16001
66.2, 4.28, 1.3459, 13, 3, 16001
66.2, 4.28, 1.3459, 13, 3, 16001
66.2,
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
2013 May 01
1
help understanding hierarchical clustering
Hi All,
i've problem to understand how to work with R to generate a hierarchical clustering
my data are in a csv and looks like :
idcode,count,temp,sal,depth_m,subs
16001,136,4.308,32.828,63.46,47
16001,109,4.31,32.829,63.09,49
16001,107,4.302,32.822,62.54,47
16001,87,4.318,32.834,62.54,48
16002,82,4.312,32.832,63.28,49
16002,77,4.325,32.828,65.65,46
16002,77,4.302,32.821,62.36,47
2006 May 24
1
dendrogram plotting problem
Dear List
RGui Version : 2.3.0
User : 1 month
I am having the *dendrogram plotting problem *
The code i tried:
>library(cluster)
DD<-DataSetS01022 # 575 x 2 matrix
> VC<-hclust(dist(DD),"ave")
*Warning message:
NAs introduced by coercion* ( what does it mean? Is that the problem?)
> plot(VC,hang=-2)
Output: http://roughjade.blogspot.com
Can anyone guide me? Thanks
2005 Jul 26
0
Hierarchical clustering with centroid method
Dear everybody!
In the function hclust, at each stage distances between clusters are recomputed by the Lance-Williams dissimilarity update formula according to the
particular clustering method being used.
Using "centroid" method, Lance-Williams recurrence formula works properly only for euclidean distance.
How is it possible to use properly centroid method with manhattan distance ?
2007 Nov 29
1
coloring leaves in clustering
Hello everyone,
I wanted to know if it was possible to change the color of certain leaves in
a hclust object in order to make my graph more readable. I know I can color
certain groups but I would like to enter a vector telling the plot function
which leaves to color in which color.
Thanks in advance,
Eleni
[[alternative HTML version deleted]]
2006 Aug 15
1
Hierarchical clustering
Hi,
I'm new to R; this is my second email to this forum. I have a dataset that
looks like this:
Gene A B
C D
A 511 6116
1515 1515
B 164 115
1515 494
C 21646
D
2013 Mar 28
2
hierarchical clustering with pearson's coefficient
Hello,
I want to use pearson's correlation as distance between observations and
then use any centroid based linkage distance (ex. Ward's distance)
When linkage distances are formed as the Lance-Williams recursive
formulation, they just require the initial distance between observations.
See here: http://en.wikipedia.org/wiki/Ward%27s_method
It is said that you have to use euclidean