similar to: Customizing Cluster Analysis plots created with hclust

Displaying 20 results from an estimated 4000 matches similar to: "Customizing Cluster Analysis plots created with hclust"

2007 Mar 09
1
dendrogram again
Hi all, ok, i know i can cut a dendrogram, which i did. all i get is three objects that a dendrograms itself. for example: myd$upper, myd$lower[[1]], myd$lower[[2]] and so on. of course i can plot them seperately now. but the lower parts still have hundreds of branches. i?ll need a 30 " widescreen to watch the whole picture. what i?d like to is group the lower branches , so that i get a
2004 May 19
7
Help with hclust() and plot()
Hi When I use plot(hclust(dist..)...)...) etc to create a dendrogram of a hierarchial cluster analysis, I end up with a vertical tree. What do I need to do to get a horizontal tree? Also, my users are used to seeing trees who's leaves all "end" at the same place (eg. Like in minitab). Is this possible in R? Thanks Mick Michael Watson Head of Informatics Institute for Animal
2017 Mar 23
1
A question on stats::as.hclust.dendrogram
Hi all, This is the first time I'm writing to R-devel, and this time I'm just asking for the purpose for a certain line of code in stats::as.hclust.dendrogram, which comes up as I'm trying to fix dendextend. The line in question is at line 128 of dendrogram.R in R-3.3.3, at stats::as.hclust.dendrogram: stopifnot(length(s) == 2L, all( vapply(s, is.integer, NA) )) Is there any
2005 Jan 25
2
Plotting hclust with lot of objects
Hi! I am newbee to R and I am facing the problem in plotting the dedrogram with lot of objects. The lines and labels are overlapped very badly, and writing the graphic to postscript and zooming there is not helping either. I tried cut.dendrogram method, but getting the error that it doesn't exist even though I get the man pages for it. I would not find any solution in web as well, and I
2006 Mar 09
1
Identifying or searching for labels in a hclust/dendrogram/heatmap
Hi Sorry if this is in the help :-S I've looked at example(dendrogram) and though it gives some indication of what I want, it doesn't do all. OK, so here is what I want to do: draw a tree, and then have an action, on user-click, to either draw a sub tree or a plot of the data. I also want users to be able to search for a particular label and have it highlighted on the tree, say in
2009 Nov 16
3
Cluster analysis: hclust manipulation possible?
I am doing cluster analysis [hclust(Dist, method="average")] on data that potentially contains redundant objects. As expected, the inclusion of redundant objects affects the clustering result, i.e., the data a1, = a2, = a3, b, c, d, e1, = e2 is likely to cluster differently from the same data without the redundancy, i.e., a1, b, c, d, e1. This is apparent when the outcome is visualized
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
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)
2002 Feb 20
1
plot.hclust: strange behaviour with "manufactured" hclust object
I've been trying to get plot.hclust to work with a hclust object I created and have not had much success. It seems that there is some "hidden" characteristic of a hclust object that I can't see. This is most easily seen in the following example, where plot.hclust works on one object, but when this object is "dumped" and then re-read, plot.hclust no longer works. Is
2010 Dec 27
1
Any functions to manipulate (merge, cut, remove) hclust objects? (maybe through phylo?)
Hello all, I'm now working with hclust objects and was hoping to perform some basic editing on them like: - Joining = the merging of two hclust objects (so they will share one root) - Splicing = So to cut/extract a branch out of an hclust object - that by itself will be an hclust object. I noticed I could extract one element of an hclust object by turning it into a dendrogram,
2011 Sep 13
2
help with hclust and cutree
Hello, I would like to cut a hclust tree into several groups at a specific similarity. I assume this can be achieved by specifying the "h" argument with the specified similarity, e.g.: clust<-hclust(dist,"average") cut<-cutree(clust,h=0.65) Now, I would like to draw rectangles around the branches of the dendrogram highlighting the corresponding clusters, as is done by
2008 May 16
2
heatmap on pre-established hclust output?
Hi, Can someone please guide me towards how to produce "heatmap" output from the output of "hclust" run prior to the actual "heatmap" call? I have some rather lengthy clustering going on and tweeking the visual output with "heatmap" recalculating the clustering every time is not feasible. Thanks, Joh
2012 Mar 29
2
hclust and plot functions work, cutree does not
Hi, I have the distance matrix computed and I feed it to hclust function. The plot function produces a dense dendrogram as well. But, the cutree function applied does not produce the desired list. Here is the code x=data.frame(similarity_matrix) colnames(x) = c(source_tags_vec) rownames(x) = c(source_tags_vec) clust_tree=hclust(as.dist(x),method="complete") plot(clust_tree)
2012 May 24
4
Manually modifying an hclust dendrogram to remove singletons
Dear R-Help, I have a clustering problem with hclust that I hope someone can help me with. Consider the classic hclust example: hc <- hclust(dist(USArrests), "ave") plot(hc) I would like to cut the tree up in such a way so as to avoid small clusters, so that we get a minimum number of items in each cluster, and therefore avoid singletons. e.g. in this example, you can see
2012 May 11
1
How to re-order clusters of hclust output?
Hello, The heatmap function conveniently has a "reorder.dendrogram" function so that clusters follow a certain logic. It seems that the hclust function doesn't have such feature. I can use the "reorder" function on the dendrogram obtained from hclust, but this does not modify the hclust object itself. I understand that the answer should be within the "heatmap"
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
2003 Sep 30
2
dump/source problem with hclust object (PR#4361)
library(mva) data(USArrests) hc <- hclust(dist(USArrests), "ave") plot(hc) # OK dump(c("hc"), "tst") rm(hc) source("tst") plot(hc) # Error in plot.hclust(hc) : invalid dendrogram input The same problem occurs with dput/dget --please do not edit the information below-- Version: platform =
2011 Sep 16
1
cutree() and rect.hclust(): different labelling of classes
I've found that while cutree() and rect.hclust() make the same classes for a given height in the dendrogram, the actual labeling of the classes is different. For example, both produce the same 4 classes but class 1 according to cutree() is class 4 according to rect.hclust(). Would it be possible that future versions provide the same labeling? rect.hclust() is useful to display the classes
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
2005 Jun 03
1
Hclust question
Hey, I am running hclust on several different distance matrices and I have a question thats more about labeling. I've been looking for a way to label the edge values on the graph with their distances between them. I've been looking through the documentation and I haven't found anything yet. Anyone know if there is a way to plot 'hclust' graphs with such edge values? Or