Displaying 20 results from an estimated 10000 matches similar to: "A question:How to plot hierarchical clustering with different colors?"
2003 Aug 13
0
re: two dimentional hierarchical clustering algorithm
Dear Dr. Liaw Andy:
I have a few more questions about your heatmap function. actually heatmap is
what I am looking for.
heatmap(x, Rowv, Colv, distfun = dist, hclustfun = hclust, add.expr,
scale=c("row", "column", "none"), na.rm = TRUE, ...)
my data is a XNEW,
> dim(XNEW)
[1] 554 335
554 genes, 335 samples.
now I want to use 1-CORR as a distance
2010 May 25
1
Hierarchical clustering using own distance matrices
Hey Everyone!
I wanted to carry out Hierarchical clustering using distance matrices i have
calculated ( instead of euclidean distance etc.)
I understand as.dist is the function for this, but the distances in the
dendrogram i got by using the following script(1) were not the distances
defined in my distance matrices.
script:
var<-read.table("the distance matrix i calculated",
2009 Nov 03
1
hierarchical clustering with Jaccard index
hi,
I want to do hierarchical clustering with Jaccord index. I tried to do with vegan package for finding index and hierarchical clustering with hclust function. While doing clustering it is showing an error message as "invalid distance method". I would be grateful if anyone tells how to rectify the error.
Thanks in advance,
kind regards,
Ms.Karunambigai M
PhD Scholar
Dept. of
2011 Jun 09
1
k-nn hierarchical clustering
Hi there,
is there any R-function for k-nearest neighbour agglomerative hierarchical
clustering?
By this I mean standard agglomerative hierarchical clustering as in hclust
or agnes, but with the k-nearest neighbour distance between clusters used
on the higher levels where there are at least k>1 distances between two
clusters (single linkage is 1-nearest neighbour clustering)?
Best regards,
2011 May 11
2
hierarchical clustering within a size limit
Hello List,
I am trying to implement a hierarchical cluster using the hclust method
agglomerative single linkage method with a small wrinkle. I would like to
cluster a set of numbers on a number line only if they are within a distance
of 500. I would then like to print out the members of this list.
So far I can put a vector:
> x<-c(2,10,200,300,600,700)
into a distance matrix:
>
2014 May 16
2
Using centers of hierarchical clustering for k-means
Hi,
i have the following problem: I am using k-means algorithm for clustering.
But instead of using randomized centers, I would like to use centers created
by hierarchical clustering. So I want to apply "hclust" on my data set (in
this case the iris data), getting a solution by "cutree", calculating the
means/centers of the resulting clusters and use these centers as starting
2011 Jul 27
0
Inversions in hierarchical clustering were they shouldn't be
Hi,
I''m using heatmap.2 to cluster my data, using the centroid method for clustering and the maximum method for calculating the distance matrix:
library("gplots")
library("RColorBrewer")
test <- matrix(c(0.96, 0.07, 0.97, 0.98, 0.50, 0.28, 0.29, 0.77,
0.08, 0.96, 0.51, 0.51, 0.14, 0.19, 0.41, 0.51),
ncol=4, byrow=TRUE)
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
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
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
2008 Feb 28
0
question regarding using weights in the hierarchical/ kmeans clustering process
Hi R users!
I have a bit of a problem with using an hierarchical clustering algorithm:
a<-c(1:15)
b<-rep(seq(1:3), 5)
c<-rnorm(15, 0,1)
d<-c(sample(1:100, 15, replace=T))
e<-c(sample(1:100, 15, replace=T))
f<-c(sample(1:100, 15, replace=T))
data<-data.frame(a,b,c,d,e,f)
q<-data.frame(data$d, data$e, data$f)
q<-scale(q)
What i want to do is to use an
2012 Aug 11
1
stopping rule in hierarchical Clustering
Dear R users,
Is there a way to apply a “stopping
rule” in hierarchical Clustering? I have a data and I want to find the optimal
number of clusters while doing hierarchical clustering. I would be deeply obliged
if someone, whoever applied stopping rule, could send me the scripts. thanks in advance
Regards
Eliza botto
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2003 Nov 08
2
help with hierarchical clustering
I have a large excel file with data in it. I converted it to a 'csv' format.
I imported this dataset to R using the follownig command
mldata <- read.csv("c:\\temp\\mldata.csv", header=T)
all the column names and the rows seems to be correct.
Now that I have this object, I need to perfrom hclust. I used the following
hc <- hclust(dist(mldata), method="single")
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
2004 May 24
0
AW: non-hierarchical non-exclusive clustering of large data sets
I think the "cmeans" method in library(e1071) works better for large data sets as "fanny".
(note,not for this data: fanny has also problems with standardized large data sets - here produce fanny the same memberships for all observations; cmeans works "correctly")
Matthias
> -----Urspr??ngliche Nachricht-----
> Von: Bhaskar S. Manda [mailto:bhaskar at
2007 Oct 30
0
Stoping rule for hierarchical clustering
Hi Sir
I am new user of 'cluster' and 'amap' packages for hierarchical clustering.
I want to find the optimum number of clusters described by Mojena (1977)
'Hierarchical
grouping methods and stopping rules: An evaluation' The Computer
Journal, 20(4).
I did not find the such function for optimal choice of clusters.
Some suggestions or hints are required.
Thank you
--
2004 May 24
1
non-hierarchical non-exclusive clustering of large data sets
Hi,
I'm trying to use R to cluster words with related meanings. Does anyone
know of a non-hierarchical clustering method in R that produces
non-exclusive clusters? With non-exclusive, I mean that words should be
allowed to be part of multiple clusters. So my data matrix would look
something like:
T1 T2 T3
CLOWN_N 0 1 0
BANK_N 3 0 2
RIVER_N 0 0 2
FLOW_V 0 0 3
MONEY_N 2 0 0
PAY_V 2 0 0
The
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 ?
2005 Dec 09
1
Hierarchical Clustering Using Mutual Information
Dear R-helpers,
Is there somebody who knows if R has already a build in function for Hierarchical Clustering which uses Mutual Information as proximity measure?
Many thanks and best regards,
J.
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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