Displaying 20 results from an estimated 2000 matches similar to: "graphic of hierachical clustering"
2003 Oct 17
1
heatmap function
Hi all,
By default, the heatmap function gives an image with a dendrogram added
to the
left side and to the top. Is it possible to only add the dendrogram to
the left side
and let the order of the columns unchanged ?
I tried
heatmap(mat, col=rbg,Rowv=res.hclust$order,Colv=1:dim(mat)[[2]]).
In this case, the order of the columns are unchanged but a dendrogram
is added to the top. How can I
2003 Aug 12
1
classification with quantitative variables
Hi all,
I want to conduct a cluster analysis with quantitative variables.
More precisely, it concerns binary and non-ordered categorical
variables. For such data, various
similarity measures have been proposed, such as the Jaccard index or the
simple matching index.
So, is there a package such as mva or multiv in the case of quantitative
variables?
Could you indicate me reviews, papers or
2003 Aug 28
2
how to call a C program from R function
Hi all,
I would like to call a C program from R function. I tried to use the
.C() function
without success. I need a very simple example (such as the hello
program) to understand
how it works. Could you give a such example?
(I use the 1.7.1 Version of R with linux)
Does it work in the case of a C++ program instead of a C programm?
Best regards,
Olivier
--
2003 Oct 13
4
help with gsub and grep functions
Hi all,
Let Names a vector of chatacters. For example,
> Names
[1] "g 604 be-0 -p1 (602 matches)" "g 606 Phli-0 -p2 (517 matches)"
[3] "g 608 alu-0 (659 matches)"
I try to use gsub or grep functions for two problems :
1. First, I would like to delete all the characters between parentheses.
[1] "g 604 be-0 -p1" "g 606 be-0 -p2"
[3] "g
2008 Jun 02
1
Plotting horizontal dendrograms
I am using hclust and plot to produce dendrograms. Using my input data I am
able to complete an analysis and obtain a vertical plot.
I want to be able to plot the dendrogram horizontally.I am using version 2.6
of R and have updated my packages recently.
Using the sample script for dendrograms I can produce a horizontal plot
using the instruction horiz = TRUE in plot().
When I use the same
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
2010 Apr 17
2
Interacting with dendrogram plots, locator() or click()
I would like to explore dendrogam plots interactively. For example, click on a node and return information about all of the children of that node.
Is there a high level wrapper for locator() or click() that will return the nearest dendrogram node on a plot?
If not, is there a way to obtain the [x,y] coordinates of all the nodes on a plot?
Thanks,
David
David J. States, M.D., Ph.D.
Professor
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")
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
2009 Jun 19
1
Drawing dendrogram
Dear all,
I would like to draw a dendrogram and mark some parts/branches (by using "segments") including their labels. If I draw it without specifying the length of x axix, I am able to do that (as in My dendrogram 1 of the following codes). However, if I want to specify the x axix, I am not able to draw marking line (by using "segments") including labels (as in My dendrogram
2011 Nov 16
1
hierachical code system
Hi,
I have a hierachical code system such as the example below (the printed data are easiest to read). I would like to write a function that returns an 'imputed' data frame, ie. where the the parent values are calculated as the sum of the child values. So, for instance, STAT.01.01.06 is the sum of STAT.01.01.06.01 through STAT.01.01.06.06. The code I have written uses two for loops,
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
2008 Jul 24
1
plot.dendrogram xlim/ylim
list(...),
I would like to zoom in to the leaves of large trees in a dendrogram
plot. The playwith package allows zooming by passing xlim and ylim
arguments to the plot call (Hmisc does this too I think). But
currently stats:::plot.dendrogram does not accept xlim or ylim. So I
would like to enable that. In place of the existing code chunk:
xlim <- c(x1 - 1/2, x2 + 1/2)
ylim <- c(0,
2004 May 06
1
question about plot.dendrogram
hi all,
i'm trying to plot a dendrogram with labeled leaves
>rownames(f)<-v.names
>v<-rowMeans(f, na.rm=T)
>clust<-hclust(dist(v))
>dend<-as.dendrogram(clust,hang=0.05)
>clust2<-cut(dend, h=0.5)
>class(clust2$low[[1]])
>[1] "dendrogram"
then
>plot(clust2$low[[1]],horiz=TRUE,frame=F,type = "tr"))
but my leaf labels do not fit
2008 Nov 21
2
Dendrogram labels
Is there any way to change the orientation of the labels on the end of the dendrograms to horizontal rather than vertical? If so, how can I do that.
_____________________________________________
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute - Webb Lab
333 Bostwick Avenue NE
Grand Rapids, MI 49503
ph. 616.234.5787
This email message,
2007 Aug 06
0
cannot use winedbg on ubuntu feisty ?
Hi everyone,
This happens every time I start winedbg, no matter what program
I want to debug. It's ubuntu feisty fawn and I have built
wine from sources.
user@machine:~$ winedbg "C:\Program Files\Diablo II\Diablo II.exe"
WineDbg starting on pid 000a
wine: Unhandled page fault on read access to 0x00000000 at address
0xb7d5cc23 (thread 0009), starting debugger...
Unhandled exception:
2008 May 06
1
Dendrogram label size
Is it possible to resize the labels in a dendrogram without applying
circles and triangles to edges?
I tried cex.labels:
plot(scoreDendogramObj, horiz=TRUE, axes=FALSE, cex.labels=0.8)
but that didn't have any effect.
Thanks,
Alex
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
2004 Jul 19
1
Dendrogram plotting options?
Hi, I was wondering if there is more flexibility in the output of
dendrograms when plotting a hclust object. I can't seem to find
information on how to change the default output of a "hanging" style
tree with the axis on the right to a left-to-right plot with and axis
on the bottom. Example code follows:
library(vegan) #loads the "vegan" module that compuptes ANOSIM
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