Re: [R] Clustering algorithms don't find obvious clusters
Le 11/06/2010 12:45, Henrik Aldberg a écrit : I have a directed graph which is represented as a matrix on the form 0 4 0 1 6 0 0 0 0 1 0 5 0 0 4 0 Each row correspond to an author (A, B, C, D) and the values says how many times this author have cited the other authors. Hence the first row says that author A have cited author B four times and author D one time. Thus the matrix represents two groups of authors: (A,B) and (C,D) who cites each other. But there is also a weak link between the groups. In reality this matrix is much bigger and very sparce but it still consists of distinct groups of authors. My problem is that when I cluster the matrix using pam, clara or agnes the algorithms does not find the obvious clusters. I have tried to turn it into a dissimilarity matrix before clustering but that did not help either. The layout of the clustering is not that important to me, my primary interest is the to get the right nodes into the right clusters. Hello Henrik, You can use a graph clustering using the igraph package. Example: library(igraph) simM-NULL simM-rbind(simM,c(0, 4, 0, 1)) simM-rbind(simM,c(6, 0, 0, 0)) simM-rbind(simM,c(0, 1, 0, 5)) simM-rbind(simM,c(0, 0, 4, 0)) G - graph.adjacency( simM,weighted=TRUE,mode=directed) plot(G,layout=layout.kamada.kawai) ### walktrap.community wt - walktrap.community(G, modularity=TRUE) wmemb - community.to.membership(G, wt$merges, steps=which.max(wt$modularity)-1) V(G)$color - rainbow(3)[wmemb$membership+1] plot(G) I hope it helps Etienne Sincerely Henrik [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] colored PCA biplot
Hillary Cooper a écrit : Hi- I'm trying to make my PCA (princomp) colored. In my csv excel sheet, I have the first column numbered according to the groupings I want to assign to the PCA. I've played around with trying to set this first column as the color vector, but haven't had any luck. Any suggestions? Thanks, Hillary Hellor Hillary, Here is some modifications of my own DIY code, the thing to do is to test it and compare with the original biplot and with what you want. I hope it helps Etienne #my.data is your/my data # I create some groups just for the test groups = sample(1:3,N,replace=TRUE) N = nrow(my.data) acp=princomp(my.data,cor=TRUE) # The original biplot for comparison biplot(acp) # Compute de min/max of new coordinates xmin = min(acp$scores[,1]) xmax = max(acp$scores[,1]) ymin = min(acp$scores[,2]) ymax = max(acp$scores[,2]) plot(c(xmin,xmax),c(ymin,ymax),col=white, xlab=Comp 1, ylab=Comp 2) # Plot the points with colors text(acp$scores[,1],acp$scores[,2],1:N,col= groups) title(PCA with colors) abline(v=0,lty=2) abline(h=0, lty=2) # Compute and apply a re-scaling for the arrows of old components # xl.min for min of xloadings,... xl.min = min(0,min(acp$loadings[,1])) xl.max = max(0,max(acp$loadings[,1])) yl.min = min(0,min(acp$loadings[,2])) yl.max = max(0,max(acp$loadings[,2])) xl.scale = max(abs(xmax),abs(xmin))/max(abs(xl.max),abs(xl.min))*0.75 # 0.75 factor is just for leave some place for the text yl.scale = max(abs(ymax),abs(ymin))/max(abs(yl.max),abs(yl.min))*0.75 #Draw old components arrows(rep(0,100),rep(0,100),acp$loadings[,1]*xl.scale, acp$loadings[,2]*yl.scale) # Names of old components text(acp$loadings[,1]*xl.scale*1.25, acp$loadings[,2]*yl.scale*1.25 ,colnames(my.data)) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] legend with small colored boxes
Christophe Dutang a écrit : Hi all, I tried to a nice legend with small boxes filled with the colors used for the plots. But it does nor work, boxes are always filled with black. An example is here plot(1:4,1:4) lines(1:4,4:1, col=blue) #try something like this legend(top,leg=c(a,b),fill=1:2) Etienne legend(top,leg=c(a,b),col=c(black,blue), fill=TRUE) How could I specify the colors? the argument col.box is the color of the whole legend box... Thanks in advance Christophe PS : I work with R 2.9.0. -- Christophe Dutang Ph. D. student at ISFA, Lyon, France website: http://dutangc.free.fr [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] truehist and density plots
Perhaps like this : temp =density(b[20:50]) truehist(b, ymax=max(temp$y)) lines(temp) Etienne carol white a écrit : Consider a vector of 100 elements (attached files). then, truehist(b) lines(density(b[20:50])) How is it possible to have density plots of all subsets like b[20:50] within histogram (without exceeding the max of historgram on y axis)? Is it more clear? Best, --- On Tue, 4/28/09, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: From: Uwe Ligges lig...@statistik.tu-dortmund.de Subject: Re: [R] truehist and density plots To: carol white wht_...@yahoo.com Cc: r-h...@stat.math.ethz.ch Date: Tuesday, April 28, 2009, 5:42 AM carol white wrote: Hi, I wanted to plot the histogram of a vector and then, plot the density function of subsets of the vector on the histogram. So I use truehist in MASS package and lines(density) as follows: length(b) = 1000 truehist(b) lines(density(b[1:100])) I do not undertsand what you mean. Can you please provide a *reproducible* example? Uwe Ligges however the density plot of the first 100 points exceeds the max of y axis (see attached). how is it possible to make a graphics so that the density plot of the subsets doesn't go beyond the maximum of all points in the complete set? Cheers, Carol __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to create a graph layout?
At 02:32 27/04/2009, Christian Bustamante wrote: I all, I want to create a graph layout in a 3x3 matrix like this: ylab |__| |__| |__| ___ ___ ___ ylab |__| |__| |__| ___ ___ ___ ylab |__| |__| |__| xl xl xl With this layout, then I'll insert the 9 plots. How ca I create it? see ?layout # Example layout(matrix(1:9,ncol=3, byrow=TRUE)) for(i in 1:9) plot(density(rnorm(1000)), main=paste(Graph N°,i)) Hope it helps. Etienne -- CdeB __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. + + Cuvelier Etienne + Assistant + FUNDP - Faculté d'Informatique + rue Grandgagnage, 21 B-5000 Namur (Belgique) + tel: 32.81.72.49.75fax: 32.81.72.49.67 + skype: cuvelier.etienne THE TOP TEN REASONS TO BECOME A STATISTICIAN 1. Deviation is considered normal. 2. We feel complete and sufficient. 3. We are mean lovers. 4. Statisticians do it discretely and continuously. 5. We are right 95% of the time. 6. We can legally comment on someone's posterior distribution. 7. We may not be normal but we are transformable. 8. We never have to say we are certain. 9. We are honestly significantly different. 10 No one wants our jobs. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to send email with R
See http://finzi.psych.upenn.edu/R/Rhelp02/archive/113531.html Etienne At 12:43 27/04/2009, Thomas Loridan wrote: Hi all I can t seem to find a way to send an email using R would anyone have a suggestion? much appreciated Thomas -- Thomas Loridan King's College email: thomas.lori...@kcl.ac.uk webpage:http://geography.kcl.ac.uk/micromet/tloridan/index.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. + + Cuvelier Etienne + Assistant + FUNDP - Faculté d'Informatique + rue Grandgagnage, 21 B-5000 Namur (Belgique) + tel: 32.81.72.49.75fax: 32.81.72.49.67 + skype: cuvelier.etienne THE TOP TEN REASONS TO BECOME A STATISTICIAN 1. Deviation is considered normal. 2. We feel complete and sufficient. 3. We are mean lovers. 4. Statisticians do it discretely and continuously. 5. We are right 95% of the time. 6. We can legally comment on someone's posterior distribution. 7. We may not be normal but we are transformable. 8. We never have to say we are certain. 9. We are honestly significantly different. 10 No one wants our jobs. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] figure layout
hesicaia a écrit : Hello, I have a specific question regarding figure layout. I am tryng to make a 2 by 1 figure but I would like to make the bottom figure slightly larger than the top figure. I have read through the help posts and have tried to use fig=c(),new=T and have also tried to use split.screen and although they both work for most types of plotting(ie. hist, plot, etc...), for some strange reason, they do not function when I try to use them with the metaplot function in package rmeta. The plot come out ok, but they are on two separate pages instead of the same one. I realize this is a very specific question, but was hoping someone might be able to suggest how I could achieve this. Below is my code for both fig and split.screen, minus the axis labels which take up a lot of space in the code. Thanks very much, Daniel. You can try to use the layout function: ?layout #Example 1 # First plot take 3/5 of the screen # Second plot 5/5of the screen layout(matrix(c(0,1,1,1,0,2,2,2,2,2),nrow = 2, byrow=TRUE)) plot(density(rnorm(1000))) plot(density(rnorm(1000))) #Example 2 # First plot take 4/6 of the screen # Second plot 6/6of the screen layout(matrix(c(0,1,1,1,0,2,2,2,2,2),nrow = 2, byrow=TRUE)) plot(density(rnorm(1000))) plot(density(rnorm(1000))) ... I hope it helps. Etienne *** library(rmeta) meta.n-meta.summaries(ttable.n$lin.yeff,ttable.n$lin.se,method=random) conf.n-1/(meta.n$se.summary^2) meta.c-meta.summaries(ttable.c$lin.yeff,ttable.c$lin.se,method=random) conf.c-1/(meta.c$se.summary^2) bitmap(/scratch/dboyce/nmfs/figs/yeareffs.all.metaplot.dev.pdf,type=pdfwrite,res=800,height=6,width=6,pointsize=12) par(mfrow=c(2,1),mar=c(1,2,1,1),oma=c(4,6,.5,.5),cex.axis=.8,fig=c(0,1,.6,1)) metaplot(mn=ttable.n$lin.yeff,se=ttable.n$lin.se,nn=(ttable.n$dev)-.05,labels=NULL,conf.level=0.95,summn=meta.n$summary,sumse=meta.n$se.summary,sumnn=conf.n/700,logeffect=F,colors=meta.colors(box=firebrick3,lines=gray38,zero=black,summary=blue,text=black),xlim=c(-.06,.16),cex=1.2,ylab=,summlabel=,xaxt=n) axis(side=1,at=seq(-.06,.16,by=.03),labels=T) text(-.06,0.5,A,cex=1.4) box() par(fig=c(0,1,0,.6),new=T) metaplot(ttable.c$lin.yeff,ttable.c$lin.se,nn=ttable.c$dev,labels=NULL,conf.level=0.95,summn=meta.c$summary,sumse=meta.c$se.summary,sumnn=conf.c/7000,logeffect=F,colors=meta.colors(box=firebrick3,lines=gray38,zero=black,summary=blue,text=black),xlim=c(-.02,.06),cex=1.2,summlabel=,ylab=,xaxt=n) text(-.02,0.5,B,cex=1.4) axis(side=1,at=seq(-.02,.06,by=.01),labels=T) mtext(Instantaneous rate of change,side=1,line=3,cex=1.5) box() dev.off() split.screen(figs=c(2,1),erase=F) screen(1) metaplot(mn=ttable.n$lin.yeff,se=ttable.n$lin.se,nn=(ttable.n$dev)-.05,labels=NULL,conf.level=0.95,summn=meta.n$summary,sumse=meta.n$se.summary,sumnn=conf.n/700,logeffect=F,colors=meta.colors(box=firebrick3,lines=gray38,zero=black,summary=blue,text=black),xlim=c(-.06,.16),cex=1.2,ylab=,summlabel=,xaxt=n) screen(2) par(new=T) metaplot(ttable.c$lin.yeff,ttable.c$lin.se,nn=ttable.c$dev,labels=NULL,conf.level=0.95,summn=meta.c$summary,sumse=meta.c$se.summary,sumnn=conf.c/7000,logeffect=F,colors=meta.colors(box=firebrick3,lines=gray38,zero=black,summary=blue,text=black),xlim=c(-.02,.06),cex=1.2,summlabel=,ylab=,xaxt=n) close.screen(all=T) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] map of china without regions
Hello, I use the map package in conjunction with the mapdata package, and I want to draw the map of China without interior regions. After reading the doc and searched in this mailing list I've tried map(china,interior=FALSE) and map(china,fill=TRUE) but I allways see the interior regions... If someone can help me... Thanks Etienne __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] debug/mtrace problem
Hello,
In the past I have used intensively the mtrace function from the debug
package, but now with my actual version of R(2.8.1) , it is impossible
to use it anymore.
I've updated all my packages, and I don't understand how solve this
problem...
Here is an example code :
foo-function(){cat(Test Function)}
mtrace(foo)
foo() # A tcl/tk windows open and close immediately
Erreur dans FUN(l[[1L]], ...) :
l'argument l est manquant, avec aucune valeur par défaut
#argument l is missing without default value...
I've tried to look in with traceback(), but it does not help me.
traceback()
21: FUN(l[[1L]], ...)
20: lapply(savers, get, envir = nlocal.env)
19: mlocal(index(nchar(names(line.list)) 0)[l] - 1)
18: screen.line(lno)
17: assign(answer, {
Here is some technical informations :
Sys.info()
sysname release versionnodename
Windows Vista build 6001, Service Pack 1 XXX-HOME-VISTA
machinelogin user
x86 xxx xxx
R.Version()
$platform
[1] i386-pc-mingw32
$arch
[1] i386
$os
[1] mingw32
$system
[1] i386, mingw32
$status
[1]
$major
[1] 2
$minor
[1] 8.1
$year
[1] 2008
$month
[1] 12
$day
[1] 22
$`svn rev`
[1] 47281
$language
[1] R
$version.string
[1] R version 2.8.1 (2008-12-22)
Sincerely
__
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