Displaying 20 results from an estimated 10000 matches similar to: "what does Height represent?"
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",
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 Oct 19
1
plot.dendrogram and plot.hclust ZOOM into the height?
Hi,
I clustered a distance matrix and would like to draw it using
plot.hclust or plot.dendrogram.
The dendrogram is not informative because I have a few extremely small
dissimilarities in the distance matrix (e.g. 0), but most of the other
distances are in the range 1e10+-5000.
I would like to show the tree only for the height of 1e10+-5000 but
unfortunately their are no parameter like
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
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 <-
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
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
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
2004 Jun 17
1
Re: Clustering in R
Thanks a lot, Michael!
I cc to R-help, where this question really belongs {as the
'Subject' suggests itself...} -- please drop 'bioconductor' from
CC'ing further replies.
>>>>> "michael" == michael watson (IAH-C) <michael.watson at bbsrc.ac.uk>
>>>>> on Thu, 17 Jun 2004 09:16:59 +0100 writes:
michael> OK, admittedly it
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"
2007 Apr 25
1
heatmap and phylogram / dendogram ploting problem, ape package
I am having trouble displaying a dendrogram of evolutionary
relationships (a phylogram imported from the ape package) as the
vertical component of a heatmap, but keeping the hierarchical
clustering of the horizontal component. The relationships of the
vertical component in the generated heatmap are not that of the
dendrogram, although the ordering is.
In more detail, I am attempting to generate
2004 Dec 15
1
hclust and heatmap - slightly different dendrograms?
Good afternoon,
I ran heatmap and hclust on the same matrix x (strictly, I ran
heatmap(x), and hclust(dist(t(x))), and realized that the two
dendrograms were slightly different, in that the left-right
arrangement of one pair of subclusters (columns) was reversed in the
two functions (but all individual columns were grouped correctly).
Looking through the code for heatmap as a most definite
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
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:
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,
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
2002 Apr 29
2
cluster analyses
I'm clustering rather large data sets and would like to cut the dendrograms
to get a better view of specific components. I calculate the dissimilarity
matrix using daisy() because I have a mixture of variable types: factors,
ordered factors and numerical variables. If I want one dendrogram, I use
agnes() for the agglomerative nesting and pltree() to draw the dendrogram.
That way, I get the
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
2003 Dec 11
1
cutree with agnes
Hi,
this is rather a (presumed) bug report than a question because I can solve
my personal statistical problem by working with hclust instead of agnes.
I have done a complete linkage clustering on a dist object dm with 30
objects with agnes (R 1.8.0 on
RedHat) and I want to obtain the partition that results from a cut at
height=0.4.
I run
> cl1a <- agnes(dm, method="complete")
2003 Dec 11
1
cutree with agnes
Hi,
this is rather a (presumed) bug report than a question because I can solve
my personal statistical problem by working with hclust instead of agnes.
I have done a complete linkage clustering on a dist object dm with 30
objects with agnes (R 1.8.0 on
RedHat) and I want to obtain the partition that results from a cut at
height=0.4.
I run
> cl1a <- agnes(dm, method="complete")