similar to: Specific criteria for color palette using heatmap.2

I'm suppressing the labeling of my rows and columns in heatmap.2 using the commands: labRow = " ", labCol = " " But I'd like to annotate them again using the axis command: axis(1, at=seq(500, 1000, 500)) mtext("Group 1", "Group 2") For some reason however it appears that the axis command is having no effect. My complete

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",

The function heatmap() allows to specify row/column labels via the options labRow/labCol. From the code of heatmap(), I understand that when no labels are specified, the row/column labels (or indices) of the input matrix are taken as labels and re-ordered together with the rows and columns of the matrix before plotting, whereas labels supplied via labRow/labCol are plotted in the original order.

Dear All, There might be a bug in heatmap(): x <- matrix(rnorm(10*5), 10, 5) heatmap(x, labCol=1:5) Error in axis(1, 1L:nc, labels = labCol, las = 2, line = -0.5, tick = 0, : 'at' and 'labels' lengths differ, 5 != 10 Works fine under 4.0.1. Looking at the code from 4.0.1 vs. Rdevel, esp. this part sticks out: labRow <- labRow[rowInd] %||% rownames(x) %||%

I have written a wrapper for heatmap.2 called heatmap.w.row.and.col.clust which auto-generates breaks using breaks<-round((c(seq(from=(-20 * stddev), to=(20 * stddev))))/20, digits = 2) #(stddev in this case = 2.5) This has always worked well in the past but now I am getting an error that non-finite breaks are being generated. Drilling down, it seems that my wrapper is generating finite

I have a file of the following form -11 -10 -9 -8 -10 -9 -8 NA -9 -7 NA NA -8 NA NA NA So basically a NxN matrix of log scores. I want to get a heatmap of these log scores but I'm having a problem. I'm using the following code library(gplots) data=read.table("filein.txt",header=FALSE) mat=as.matrix(data) heatmap.2(mat,dendrogram=c("none")) But on the

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,

I am using heatmap with the arguments below. The title size stays the same no matter what I set cex.main to. Is this expected? Can I adjust the title size in heatmap? Also, the position of the main title is at the very upper edge of the output and if I use a "\n" to stack the title the upper line is out of bounds and doesn't show up. I am outputting to pdf. Any help? Thanks,

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, dendrogram = c("both"), scale = c("row"), na.rm=TRUE, trace="none",

Dear R users, need help with my heatmap. I will really approciate some help. Given the matrix: > head(x) A B C D time [1,] 0 8 0 0 1 [2,] 0 160 0 0 2 [3,] 0 175 0 0 3 [4,] 0 253 0 0 4 [5,] 79 212 0 0 5 [6,] 6 105 0 0 6 and call: ##------------ Heatmap -------------- library(RColorBrewer) rc <- grey((nrow(x):1)/nrow(x)) heatmap(data.matrix(x[,1:4]),

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, How do I anchor z=0 to the white color in a levelplot so that the color changes from cyan to magenta precisely as z changes from negative to positive? Also is it easy to change color scheme, say to blue/red as it's more dramatic? Is there a better function for showing heatmap with a color bar? Thanks in advance for any help, I've played with image, heatmap and levelplot a little and

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

Hello, I have come across some unexpected behaviour of the function heatmap in the stats package. This looks like a bug to me, but I might have misunderstood something. When calling the function in symmetric mode, the ColSideColors are plotted correctly, but RowSideColors appear in reverse order. This code (modified from the example on the help page) demonstrates the problem: cU <-

Good afternoon, I ran heatmap and hclust on the same matrix x (strictly, I ran heatmap(x), and hclust(dist(t(x))), and realized that the two dendrograms were slightly different, in that the left-right arrangement of one pair of subclusters (columns) was reversed in the two functions (but all individual columns were grouped correctly). Looking through the code for heatmap as a most definite

I would like to use gridBase to place four separate heatmaps (actually, a stripped-down heatmap.2 from ght gregmisc package that contains only the "image" part) into four different viewports. I can get the placement correct, but I keep 'losing' the previous plot. Any suggestions? Here is some quick example code trying to put a heatmap into the left viewport and then

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

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 wanted to make more than one side color bar. For example, I can make one side color bar (col1) with the following code: ----------------------------------- library(gplots) mat <- matrix(sample(1:100,40),nrow=5) class1 <- c(rep(0,4),rep(1,4)) col1 <- ifelse(class1 == 0,"blue","red") class2 <- c(rep(1,3),rep(2,5)) col2 <- ifelse(class2 ==