similar to: row lables in heatmap.2()

Dear list, I am using heatmap.2(x) to draw a heatmap. Ideally, I want to the matrix x clustered only by columns and keep the original order of rows unchanged. Is there a way to do that in heatmap.2()? Thanks a lot! Any suggestions will be appreciated! Best, Allen [[alternative HTML version deleted]]

Hi friends, I used heatmap(as.matrix(y2),col=rainbow(256),scale = "column") to generate the heatmap. But it did not show the code that which color correspond the value. Is there any parameter for this in heatmap()? Thanks a lot! Allen [[alternative HTML version deleted]]

Hi list, My data set is comprised of 47 columns and about 700 rows. Most of the values would be around 2, while some will go beyond in either direction, higher or lower. Is there a way to specify the parameter of col or others if necessary to have the range of representing colors be 0----8, and make dark for 2, red for higher than 2 and green for lower than 2. Is there a way to do this? Thanks a

Hello list, I read in a txt file using <B<-read.table(file="data.snp",header=TRUE,row.names=NULL) by specifying the row.names=NULL so that the rows are numbered. Below is an example after how the table looks like using <B[1:10,1:3] SNP Chromosome PhysicalPosition 1 SNP_A-1909444 1 7924293 2 SNP_A-2237149 1 8173763

Hi Chakravarthy, [dont forget to Cc the list for useRs with the same Q.] If you're trying to reuduce the isze of your row or column labels, i think the following arguments of heatmap.2 {gplots} is what you want to adjust- 'cexCol' and 'cexRow'. Specifically on my question that you ask about, i found the BioC forum helpful:

Dear list, I need to read in a big table with 487 columns and 238,305 rows (row names and column names are supplied). Is there a code to read in the table in a fast way? I tried the read.table() but it seems that it takes forever :( Thanks a lot! Best, Allen

Hello all- I am having trouble with the cell sizes that heatmap defaults too. I have a matrix of 160 rows and 5 columns that I am trying to display with heatmap(). When I do this, the cells default to really wide and very short. This makes the labels for the rows very hard to read, in fact the only way I can read them is to make the jpeg output very large and zoom in, and even then it's hard

Hi Allen and list, See the code below.? I've tried it on R2.13 and R2.8.0 using either heatmap.plus 1.3 or the latest.? All gave the same results.? The problem is in the last line: when I tried to plot two different color bars, the one corresponding to "cm.colors(10)" is not correct (it starts with one black and one red.? Not sure where they're from?) Any ideas? Thanks!

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",

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

Hello list, I have a data frame M like: BAC chr pos s1 s2 RP11-80G24 1 77465510 -1 0 RP11-198H14 1 78696291 -1 0 RP11-267M21 1 79681704 -1 0 RP11-89A19 1 80950808 -1 0 RP11-6B16 1 82255496 -1 0 RP11-210E16 1 228801510 0 -1 RP11-155C15 1 230957584 0 -1 RP11-210F8 1

Esteemed R user's, I'm struggling to achieve some details of a heatmap using heatmap.2(): 1. Change label locations, for both rows & columns from the default right & bottom, to left and top. Can this be done within heatmap.2()? Or do i need to suppress this default behavior (how) and call a new function to relabel (what) specifying locations? 2. Change the angle of the

Hi Kevin, >>>>> "krc" == krc <krc at odin.mdacc.tmc.edu> >>>>> on Mon, 27 Jun 2005 21:55:37 +0200 (CEST) writes: krc> Full_Name: Kevin R. Coombes krc> Version: 2.1.0 krc> OS: Windows XP krc> Submission from: (NULL) (143.111.224.169) krc> When revC = TRUE and RowSideColors is set to a list of krc>

> Dear list, > I have a data frame like: > > > log2.ratios[1:3,1:4] > ID a1 a2 a3 > 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 > 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 > 3 RP11-62M23 -0.1761700 0.08214500 -0.04877000 > 4 RP11-62M23 0.2761700 -0.15214500 -0.05877000 > the 3rd and

Full_Name: Kevin R. Coombes Version: 2.1.0 OS: Windows XP Submission from: (NULL) (143.111.224.169) When revC = TRUE and RowSideColors is set to a list of colors in heatmap, then the image and dendrogram are inverted, but the row-side color map does not change. The following script illustrates the problem. ############## set.seed(1023) # generate columns of two different types d1 <-

Howdy, I am trying to make a simple monochrome heatmap from 1 row of data. Essentially, I just want a long bar where black represents the max value in the data, white is the minimum, and all values in between are interpolated appropriately. I have tried using heatmap and heatmap.2, but both have issues. heatmap seems to be restricted to only drawing a square plot, and this data requires a

Hello R Gurus, I have a matrix for which I am doing a heatmap using heatmap.2. I want to put the rownames on the lefthand side instead of the right side of the heatmap. how can i put the rownames on left hand side: I have already tried axis but could not make it work ccc<-structure(c(1, 0.283300333755851, 0.237863231117007, 0.0148696794159253, -0.0780756406815149, -0.106161465097659,

Full_Name: Peter Fischer Hallin Version: Version 1.8.1 OS: Irix64 Submission from: (NULL) (130.225.67.236) I've made a script look like this: exp <- read.table("graph/1933672048.cluster.data") exp <- as.matrix(exp) postscript("graph/1933672048.cluster.data.ps") heatmap(exp,scale="none",cexCol=0.4,cexRow=0.2,col=custom,margins=c(5,5)) The row labels

Hi list, Is there a way to read in a txt file with some blanks? The ideal way could be to replace blanks with NAs. Thanks a lot! Allen [[alternative HTML version deleted]]

> Dear expeRts, > > Currently, my colors are as follows: > mycol <- > c("blue1","blue2","blue3","blue4","black","yellow4","yellow3","yellow2","y > ellow1") > heatmap(snp, Rowv=NA, Colv=NA, col=mycol) > > However, I would like to have the following colors: > bright blue ->