similar to: Drawing Heatmap using gplots

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 = dist, hclustfun = hclust, dendrogram = c("row"), scale =

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 ) segments(86, 0 ,270,col = "green", pch=23,

Dear all, I have an issue trying to install new packages (have tried with RODBC_1.3-1, gplots_2.6.1, gtools_2.7.4 packages) and get the same error message : "Error in library(gplots) : there is no package called 'gplots'" Only clue I have found so far on the Web is related to Perl (Perl modules are installed on my computer, but which one is related to gplots if any ?); no

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 %<81>â<81>ã<81>Ï<81>Ó\r 1 0 obj << /CreationDate (D:20100902122215) /ModDate (D:20100902122215) /Title (R Graphics Output) /Producer (R 2.11.1) /Creator (R) how to reconvert it to the my actual code?? as I do not have backup for

Hi all, I think the code to calculate the default value of the symbreaks argument in the gplots::heatmap.2 function is wrong. The documentation says symbreaks defaults to true if any negative values are detected in the data passed in. The relevant code in the parameter list of this function definition (gplots 2.7.3) is this: symbreaks = min(x < 0, na.rm = TRUE) || scale !=

When I try to install the ROCR package (which requires gplots) on Ubuntu 9.10 (Xubuntu Karmic Koala) 64-bit on R version 2.9.2 (2009-08-24), it eats up all my RAM (2GB) and swap (4GB) and keeps allocating more memory until Linux's out of memory (OOM) killer kills the perl process. This problem is special to Ubuntu because I can install other packages (such as party) on this Ubuntu system, and

Dear list, I am trying to plot the local variance in a moving window on a dataset. The function that I am trying to use for this is wapply from gtools. However, from the lattice panel function code: <snip> cat(x) cat(y) wapply(x,y,method="range",width=1/10,fun=sd,na.rm=TRUE) -> outvar </snip> I get: <snip> 109 109 109 109 109 109 116 116 116 116 119 119 123

Dear R users, I'm trying to create images of 2 symmetrical matrices using heatmap.2 of the 'gplots' library. Both matrices have the same row and column names For the first matrix I'm using the default clustering and column denrogram options: heatmap.2(Matrix1, symm=T, breaks=20, col=rich.colors(19), main="matrix1", density.info="histogram",

Hi everyone! I get the following message anyhow I try to load the package gplots: Error in lazyLoadDBfetch(key, datafile, compressed, envhook) : ReadItem: unknown type 241 Error in library(pkg, character.only = TRUE) : package/namespace load failed for 'gplots' Could any of you tell me what goes wrong? (I am using R 2.0.1. on Windows) Thanks a lot: ----------

require(gplots) data(rtPCR) overplot( RQ ~ Conc..ug.ml. | Test.Substance, data=rtPCR, subset=Detector=="ProbeType 7" & Conc..ug.ml. > 0, same.scale=TRUE, log="xy", f=3/4, main="Detector=ProbeType 7", xlab="Concentration (ug/ml)", ylab="Relative Gene Quantification" ) # Error in lowess.default(mf[[-response]], mf[[response]], f = f,

Announcing gplots 2.5.0 --------------------------------- gplots provides additional plotting functions, including several enhanced versions of base R functions. Provided functions include: balloonplot, bandplot, barplot2, boxplot.n, colorpanel, heatmap.2, hist2d, lowess, ooplot, overplot, plot.lm2, plotCI, plotmeans, qqnorm.aov, residplot, rich.color, sinkplot, smartlegend, space,

Announcing gplots 2.5.0 --------------------------------- gplots provides additional plotting functions, including several enhanced versions of base R functions. Provided functions include: balloonplot, bandplot, barplot2, boxplot.n, colorpanel, heatmap.2, hist2d, lowess, ooplot, overplot, plot.lm2, plotCI, plotmeans, qqnorm.aov, residplot, rich.color, sinkplot, smartlegend, space,

Hi list, I found this one when I was trying to output the Venn diagram to a .pdf file.? When there are 4 sets of groups to draw, the .pdf file automatically has 3 pages and the figure only appears on the 3rd page in the .pdf file with the first 2 pages being blank.? Try the following: (I'm using R-2.9.0 on WinXP, gplots 2.7.1).? gplots 2.7.3 has the same problem.

Hello, I'm fairly new to R and am running version 2.11.0 with Windows 7. I need to run the package gplots. The package installs fine, but when I try to load it I receive the message: Loading required package: gtools Error: package 'gtools' could not be loaded In addition: Warning message: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there

Dear list, I am using R.2.11.1 version on a PC. I downloaded successfully gplots_2.8.0 but I could not find where to download caTools > library("gplots") Loading required package: caTools Error: package 'caTools' could not be loaded In addition: Warning message: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called

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), #col=greenred(75), Rowv=TRUE, Colv=FALSE, distfun = dist,

Hi, I want to take a look at the sourcecode for balloonplot. I would appreciate it if I could get help on overcoming the following problem : > methods(balloonplot) [1] balloonplot.default* balloonplot.table* ? ? ?Non-visible functions are asterisked > balloonplot.default Error: object 'balloonplot.default' not found > How do I access the non-visible functions? Thanks, Ravi??

hi all i'm trying to open gplots library but i keep on getting this error: /Loading required package: gdata Error in readRDS(mapfile) : embedded nul in string: 'ref\0\0\002\0\0\0\0' Error : unable to load R code in package ?gdata? Error: package ?gdata? could not be loaded/ if i run session info the results are: /> print(sessionInfo()) R version 2.15.1 (2012-06-22) Platform:

Hi all, I am taking this over from r-help (see http://permalink.gmane.org/gmane.comp.lang.r.general/273985). I experience a segfault when calling gplots::heatmap.2(), but only when certain other packages are loaded. I am not sure for the correct place to send this bug report. Should I send it to the package maintainers directly? If R-help is the wrong place, please feel free to direct me to

Dear R users, I have a question regarding how to make row labels readable in a heat map. I have successfully made a heat map using function "heatmap.2" in the package "gplots". However, as there are many rows in the heat map, I have difficulties labeling them (heatmap.2 provides a parameter "labRow" to label the row names, but as I have too many rows, I can not make