[R] Z score in gplots

Hi, Can anyone tell me how to set Z-score according to my own requirement as the below code is taking as per the file entries. Any help would be appreciable. library(gplots) x=read.table(final.txt, header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c(green,white,red))(256),

[R] gplot heatmap

Hi, I am drawing a heat map using gplots of R package. The file (new4) is having values 0 and 1 only. library(gplots) library(marray) x=read.table(new4, header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c(black,red))(256), #col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun =

Re: [R] venn diagramm

it with different sides and I hope I will get something of of it. But if you also extract some good plz let me know. I also got a online tool called venny to draw for 4 subsets. Thanks khush On Sat, May 7, 2011 at 10:28 PM, Breheny, Patrick patrick.breh...@uky.eduwrote: I've never actually used

[R] venn diagramm

in drawing the same any script . Thank you Khush [[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

[R] Clustering help in Heat Maps

Dear Experts, I am using the below script to generate the heat map of gene expression data. I am using Hierarchical Clustering (hclust) for clustering. Now I want to compare different clustering parameters such as *K-means* clustering, Model Based Clustering, I have two queries: 1. How to

[R] Drawing Heatmap using gplots

Hi, I am using heatmap.2 of gplots to make heatmaps of my the attached file. I am giving my code for the same .. library(gplots) x=read.table(1.txt, header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust,

[R] Drawing Heatmap using gplots

Hi, I am using heatmap.2 of gplots to make heatmaps of my the file. I am giving my code for the same .. library(gplots) x=read.table(1.txt, header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram =

[R] Argument lib is missing

-redhat-linux-gnu-library/2.11' Warning: unable to access index for repository http://cran.csdb.cn/src/contrib Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘gplots’ is not available any suggestion will be appreciable. Thank you Khush [[alternative HTML

[R] R code changes to crap

Hi, I am using vim to edit my files...I do not know what has been pressed by me as my R code get converted to such a crap... %PDF-1.4 %81â81ã81Ï81Ó\r 1 0 obj /CreationDate (D:20100902122215) /ModDate (D:20100902122215) /Title (R Graphics Output) /Producer (R 2.11.1) /Creator (R) how to

[R] Save data as .pdf or .JPG

Hi all , I have following script to plot some data. plot( c(1,1100), c(0,15), type='n', xlab='', ylab='', ylim=c(0.1,25) , las=2) axis (1, at = seq(0,1100,50), las =2) axis (2, at = seq(0,25,1), las =2) lines( c(1,304),c(0,0),col='grey', lwd=3 ) lines( c(1,238),c(1,1),col='grey', lwd=3 )

Re: [R] points marking

(Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 *From:* khush [mailto:bioinfo.kh...@gmail.com] *Sent:* Monday, June 14, 2010 11:21 PM *To:* Greg Snow *Cc:* Petr PIKAL *Subject:* Re: [R] points marking Dear Gregory

Re: [R] points marking

with the points function and the segments separately. Segments can take vectors, so you don’t need to separate things into multiple calls. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 *From:* khush

Re: [R] points marking

( x1,rev(x1) ), c(y2, rev(y3)), col='grey' ) ) -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of khush

[R] points marking

Hi, How to mark points on x axis of a graph keeping x axis as constant and changing y from y1 to y2 respectively. I want to highlight the area from y1 to y2. Any suggestions Thank you Jeet [[alternative HTML version deleted]] __

[R] rgl installation failure

Hello, I am trying to install rgl package under R and getting some errors which is below. install.packages(rgl) Warning in install.packages(rgl) : argument 'lib' is missing: using '/usr/lib/R/library' trying URL 'http://cran.csie.ntu.edu.tw/src/contrib/rgl_0.91.tar.gz' Content type

Re: [R] rgl installation failure

Thank you Jeet On Sat, Jun 5, 2010 at 1:07 PM, Berwin A Turlach ber...@maths.uwa.edu.auwrote: G'day, On Sat, 5 Jun 2010 12:51:08 +0530 khush bioinfo.kh...@gmail.com wrote: I am trying to install rgl package under R and getting some errors which is below. install.packages(rgl

[R] Shapes in barplots

Hi, I am making barplots . I am using the default shape of barplots with a pipe but I wants to build bars in various 3d shapes. I have install rgl using install.packages('rgl') for this purpose, but when I am doing library(rgl), it shows Error in library(rgl) : there is no package called 'rgl'

Re: [R] Shapes in barplots

-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of khush Sent: Friday, June 04, 2010 1:45 AM To: r-help@r-project.org Subject: [R] Shapes in barplots Hi, I am making barplots . I am using the default shape of barplots with a pipe but I wants

Re: [R] Help barplots

bp[3], 15.2 how to make a dotted line using R, is it possible Thank you in advance Jeet On Tue, Jun 1, 2010 at 4:31 PM, khush bioinfo.kh...@gmail.comwrote: Dear All, I am newbie to R, and I wanted to plot a barplots with R and in such a way that It will also show me

[R] Help barplots

Dear All, I am newbie to R, and I wanted to plot a barplots with R and in such a way that It will also show me position which I can plot on the bar line. Here is my code that I am using to plot, chromosome - c(40.2, 35.6, 36.1, 29.6, 31, 29.6, 31, 29.4, 28.2, 23, 23, 28.2) barplot (chromosome,

Re: [R] Help barplots

Dear All, Thank you very much for your kind help and support I got it. Jeet On Tue, Jun 1, 2010 at 5:32 PM, Jim Lemon j...@bitwrit.com.au wrote: On 06/01/2010 09:01 PM, khush wrote: Dear All, I am newbie to R, and I wanted to plot a barplots with R and in such a way