similar to: more color choice with heatmap.2

Dear All: I tried to use heatmap.2 to generate hierarchical clustering using the following command: heatmap.2(datamatrix, scale="row", trace="none", col=greenred(256), labRow=genelist[,1], margins=c(10,10), Rowv=TRUE, Colv=TRUE) datamatrix is subset of a RMA normalized data subset by a genelist. The problem is a lot of times, the z-score in key are from, like -5 to 15 or

Hi, i created a graph with heatmap(sma) function: heatmap(dataHeat(x)) and I wish to change the gradation of colors from blue to red, how could i do? Using "heatmap(dataHeat(x), col=c(2,4))" i will use only 2 colors without gradation. Ty so much Andrea

Has anyone tried to download Hmisc and used ldBands function for calculating Lan-Demets group sequential boundaries? The write-up in F.Harrell's website indicates that, besides downloading the package Hmisc, one needs to copy the progra ld98 from the University of Wisconsin website. As suggested, I did this but received another error message regarding the search path. I think I have fixed

Hello R-Users! I'm using a heatmap to visualize a matrix of values between -1 and 3. How can I set the colors so that white is zero, below zero is blue of increasing intensity towards -1 and above zero is red of increasing intensity towards red? I tried like this (using the marray and gplots packages from bioconductor): mcol <- maPalette(low="blue", mid="white",

Dear R Community, I am trying to create an heatmap for the following set of data: ##example of data matrix o4 V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15 V16 V17 V18 green 27 28 29 29 28 28 26 25 25 23 23 22 22 21 21 22 22 22 yellow 6 8 8 7 7 7 6 6 6 7 7 7 6 6 6 6 6 5 red 15 15 15 15 15 15 14 13 12 11 12 10 9 8 7 6 8 9 pink

I'm trying to create a graph where different cells of a grid (a shapefile) will be painted with a color share scale, where the most easy way is to use gray(). Can I somehow get a vector (gradient) of colors, a vector of colors with other methods but gray()? I'm doing this until now quad_N_sp <-

Hi All, My group is looking for any suggestions on what to purchase to achieve the most powerful number crunching system that $50k can buy. The main application that will be used is R so input on what hardware benefits R most will be appreciated. The requirements are that it be a single standalone server (i.e. not a cluster solution), and it that must be able to run unix/linux. If

Hi guys, I have a matrix with values varying from approximately -0.7 to 0.33 that I want to create a heatmap/levelplot with. When I execute the levelplot function for my matrix, I end up getting colors that are adjusted to the max and min rather than around 0. In other words, ideally I would like to have a color ramp that goes from red (negative number), to white (0), to blue (positive);

I try to use ColorRamp as ColorRampPalette (i.e. with the same gradient), but it seems there is a nuance that I've missed. pal.crp<-colorRampPalette( c("blue", "white", "red"), space = "rgb") plot(rep(0,40),pch=16,col=pal.crp(40)) # is great But, using the same gradient with colorRamp is giving erratic colors. pal.cr<-colorRamp(

Hi, I'm kinda new of the R world. I need to use the heatmap or heatmap.2 function to plot correlation values. 2 questions: - how can I specify a color palette? (would like to have a transition from blue(-1) to white(0) to red(1)) - how can I use heatmap.2 imposing a specific order (like hclust.order)? I mean, I don't want heatmap.2 to re-cluster/re-order my data but just to plot them

Dear list, I have a question on moving color keys when side color bars are added to a heatmap. The R code below produces the color key in the upper left corner. Notice I have added side bars to the heatmap, but how could I move the color key below the image? ------ library(gplots) data(mtcars) x <- as.matrix(mtcars) rc <- rainbow(nrow(x), start=0, end=.3) cc <- rainbow(ncol(x),

Hi, I'm trying to create a heatmap with color ranges for different values in my matrix. For example: If x > 5 , use orange gradient if x < 1.5, use red gradient ..... Right now I have the following: orgPal<-brewer.pal(3,"Oranges") bluPal<-brewer.pal(3,"Blues") redPal<-brewer.pal(3,"Reds") grad <- ifelse(randMat >

I'm trying to display the probability space of a function and wanted to see specifically where the maximum posterior probability is. data=read.table("PosteriorData",header=F) mat=as.matrix(data) heatmap.2(mat/max(mat,na.rm=T),dendrogram=c("none"),trace=c("none"), Rowv=F,Colv=F,labRow=3*c(10:-10),labCol=3*c(-10:10),symm=T,col=rainbow(100)) As the

Hi I made heatmap of QTL based on Lod score. Where I have traits in columns and marker data (rows). I can not cluster both column and rows as I need the right order for marker data. Can someone suggest me better way of generating heatmaps especially the colour key I want to select to visualize the results which are more interesting to look at. > library(gplots) >

HI All sorry if this question has already been asked but I couldn't find anything that answered my question I have 24 columns of data that I'm trying to plot in heatmap.2 (gregmisc) and I'm having difficulty ordering them except in numerical sequence: I have transposed my matrix so it will appear with the dendrogram I want appearing at the top of the heatmap If I use either of

hi, I have a positive integer matrix like: test<-matrix(c(1,2,2,2,2,1,1,2,3),3) and based on the distant function I made like this: generateDistMat<-function (target) { n <- nrow(target) rn <- rownames(target) distM <- matrix(NA, n, n) diag(distM) <- 0 for (i in 1:(n - 1)) for (j in (i + 1):n) { distM[i, j] <- length(which(target[i, ] !=

Hi all, I had the need to create a colorbar considering the alpha channel of the colors, but colorRamp() and colorRampPalette() ignored the alpha argument in rgb(). So I performed some minor modifs. in their codes, as to support the interpolation using the alpha channel. I guess that those simple modifications might be useful for other people, so perhaps it would be worth to add them to

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 <-

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>

Hi all, I have a matrix with values between 0 and 1. I want to plot this matrix on a heat map so anything >0.05 is blue, anything <=0.05 and >0.01 is yellow, and anything else is grey. I am using the heatmap.2 function. I searched around but did not find an efficient way to set colour ranges as I described. Could anybody give some hints? Thank you in advance. Wendy -- View this