similar to: set heatmap.2 color ranges

Dear R team, As this is a university email address with very small inbox limit, can I please change my R email subscription to another email address instead of this one? My new email address is wendy2.qiao@gmail.com. I have change my email in my profile, but seems that does not change my subscription. Thank you. Wendy [[alternative HTML version deleted]]

Hi all, I have a huge matrix of TRUE/FALSE table like following, and I want to count the number of TRUEs in each row. Instead of looping through each row and do length(Z[Z==TRUE]), I am wondering if there is an easier way of doing this. [,1] [,2] [,3] [1,]TRUE FALSE FALSE [2,]FALSE TRUE TRUE Thank you in advance. Wendy -- View this message in context:

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, I have a list of numbers, e.g., X = c(60593.23, 71631.17, 75320.1), and want to round them so the output is Y = c(60000, 80000, 80000). I tried Y<-round(X,-4), but it gives me Y = c(60000, 70000, 80000). Do anybody know how to round up a number to 10^4? Thank you in advance. Wendy -- View this message in context:

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, ] !=

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'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 >

> 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 ->

Hi all, I have a matrix, for example [,1] [,2] [1,] 1 3 [2,] 4 6 I want to replicate the matrix twice and add an extra column at the end, which is [,1] [,2] [,3] [,4] [,5] [,6] [,7] [1,] 1 3 1 3 1 3 2 [2,] 4 6 4 6 4 6 5 I found 'rep' only works for vector. Does anyone know how to replicate a matrix, and append the matrix?

Hi, I have searched for a solution but I failed to find an answer. I am hoping you may be able to help me. I have a data set where I have observations for a number of units (n =~40) over a period of time (t =~100) and I have a variable (Z) that codes a categorical variable for each observation. I want to produce a 2D plot where time is on the x-axis and units are on the y-axis. Then each block

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'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

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 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>

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, I hope to show a heatmap with thre colours, no gradation. How to specify heatmap.2 to map "green" for values less than -1, "gray" for values between -1 and 1, and "red" for values greater than 1 ? Thanks [[alternative HTML version deleted]]

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),

Hello there! I'd just like to say in advance, "Thank you," for any help and/or advice. My problem is as follows: I have a dataset that is made up of percentages. I've assigned my "error" percentages a value of '-100', my "non-existent" percentages a value of '0', and all my other percentages are normal values that range from the high

Hi,   I need to generate a heatmap on a square matrix and wouldn't want to reorder the columns and the rows on the heatmap display.    I have used the options Rowv=NULL and Colv=NULL but doesn't seem to work. Following is a snippet of the heatmap function i am using. args <- commandArgs(); inputfile <- args[2] imgfile   <- args[3] bitmap(imgfile, height=15, width=15, res=100,

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