Displaying 20 results from an estimated 10000 matches similar to: "rotate a dendrogram"
2003 Jun 23
0
heatmap
Dear R-users,
I am using R-1.7.1. on windows 2000. When I use the heatmap() function, I
found lines on the dendorgam are not well connected. For example, the two
dendrograms produced by the following have this problem.
set.seed(1234)
heatmap(x<-matrix(rnorm(100*30),100,30))
Is there a bug in plot(dendrogram object) which heatmap used?
Thanks,
Ming-Chung Li
2009 Apr 30
2
How to skip rest of code
Dear R users,
Suppose I have 2 R script files: 'test1.R' and 'test2.R' and one R file 'main.R' which sources each of them. I wonder if there is a way to skip rest of code in 'test1.R' once a condition is met but still continue to run rest of script from the 'main'R' file.
A simple example is shown below. I hope only 'message1' and
2012 Aug 12
0
Different cluster orderings from cutree() and cut.dendrogram()
Hi!
I just discovered that cutree() and cut.dendrogram() do not assign the
same cluster numberings when called on the same tree. More specifically,
cutree() assigns cluster numbers by order of appearance in the data,
while cut.dendrogram() sorts clusters by height (see example below). I
guess this is for historical reasons?
I'm hit by this difference when I want to get a vector of cluster
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
2012 Jul 31
3
[LLVMdev] rotate
Andy,
Here is the left circular shift operator patch. I apologize to the reviewer
in advance. The patch has a good bit of fine detail. Any
comments/criticisms?
Some caveats...
1) This is just the bare minimum needed to make the left circular shift
operator work (e.g. no instruction combining).
2) I tried my best to select operator names in the existing style; please
feel free to change them as
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
2002 May 15
0
RE: cut.dendrogram (PR#1552)
>>>>> "MM" == Martin Maechler <maechler@stat.math.ethz.ch> writes:
>>>>> "MikG" == M GRUM <M.GRUM@CGIAR.ORG> writes:
MikG> I'm resending this bug report with a new example. As
MikG> seen below, cut.dendrogram gives an error message for
MikG> some heights, but not for others and with some
MikG> datasets
2003 Apr 01
2
cor.test observations limit
Hi,
Is there a limit on the number of observations for using cor.test. For
example,
> library(ctest)
> cor.test(rnorm(3000), rnorm(3000), method="spearman")
Error in if (q > (n^3 - n)/6) pspearman(q - 1, n, lower.tail = FALSE) else
pspearman(q, :
missing value where logical needed
In addition: Warning message:
NAs introduced by coercion
I mainly want to calculate
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<-
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
2009 Aug 17
0
heatmap and dendrogram
Dear all,
I generated a heatmap with the heatmap() function with the default
"complete" linkage method, but when I add the argument
Rowv=as.dendrogram(hclust(dist(matrix), method="complete")),
The dendrogram generated is different from the dendrogram produced by
heatmap() with default settings. Could someone kindly point out where my
mistakes are?
P.S. When I did
2007 Dec 16
0
levelplot border and dendrogram width
Hello,
I'm trying to learn how to use lattice and levelplot in particular.
There are three elements of customizing the plots I'm stuck with:
a) Is there a way to put borders around each "cell" within a
level-plot. I'm trying to do something like the
colsep/rowsep/sepcolor/sepwidth parameters of heatmap.2 in gplots
b) Can I alter the line-width of dendrogram added
2010 Nov 15
1
plot.dendrogram() plot margins
Hello,
Is it possible to remove those extra margins on the "sample" axis from
plot.dendrogram:
par(oma=c(0,0,0,0),mar=c(0,0,0,0))
ddr<-as.dendrogram(hclust(dist(matrix(sample(1:1000,200),nrow=100))))
stats:::plot.dendrogram(ddr,horiz=F,axes=F,yaxs="i",leaflab="none")
vs.
stats:::plot.dendrogram(ddr,horiz=T,axes=F,yaxs="i",leaflab="none")
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
2002 May 14
0
RE: cut.dendrogram (PR#1552)
>>>>> "MikG" == M GRUM <M.GRUM@CGIAR.ORG> writes:
MikG> I'm resending this bug report with a new example. As
MikG> seen below, cut.dendrogram gives an error message for
MikG> some heights, but not for others and with some
MikG> datasets adn not others. I can't see why.
MikG> Last time I unwittingly sent my message with
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
2011 Apr 11
1
heatmap clustering dendrogram export
Hi,
I am a beginner for R.
I had use gplots to generate a heatmap as following:
>heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE,
trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2,
cexCol=0.6)
It work well. It generate heatmap whith rcolumn clustering dendrogram and I
can export a very nice graph. But I don not know how
2009 Jan 17
1
Dendrogram with the UPGMA method
Hi,
I am clustering objects using the agnes() function and the UPGMA
clustering method (function = "average"). Everything works well, but
apparently something is wrong with the dendrogram. For example:
x<-c(102,102.1,112.5,113,100.3,108.2,101.1,104,105.5,106.3)
y<-c(110,111,110.2,112.1,119.5,122.1,102,112,112.5,115)
xy<-cbind(x,y)
library(cluster)
UPGMA.orig<-agnes(x)
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 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