similar to: Cell size in heatmap

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

Dear R-Helpers, I have a short question related to heatmap.2 function. I wanted to change the dimension of each cell in the heatmap drawn by this function. here is a reproducible example from the help page library(gplots) data(mtcars) x <- as.matrix(mtcars) rc <- rainbow(nrow(x), start=0, end=.3) cc <- rainbow(ncol(x), start=0, end=.3) hv <- heatmap.2(x, col=cm.colors(255),

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

I've just uploaded gregmisc 0.8.6 to CRAN, it should show up in the package tree shortly. It contains both an enhanced barplot() [named barplot2 in my code] and an enhanced heatmap() function that I would like to see propagate to the base and mva packages respectively. I've checked the code for both functions against the code in R 1.8.1, and these functions have all of the latest

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, ] !=

All - Below are samples of the data, a description of my approach and the work I've done so far. My goal is two-fold, first learn more about R and the creation of heatmaps; second, to create a heat map where the vertical access is a series of days and the horizontal is the hour of a day with the color of the cells being determined by the number of texts in that hour. While the project

I generated a heatmap in R using the following commands: > mydata <- read.csv(file="Data.csv", header=TRUE, sep=",") > mydata <- mydata[rowSums(mydata[,-1]^2) >0, ] > rownames(mydata)=mydata$Name > mydata <- mydata[,2:253] > mydatamatrix <- data.matrix(mydata) > mydatascale <- t(scale(t(mydatamatrix))) > hr <-

Hi all, I have simple x/y data from screen recording in a sequence: number,x,y ---------------- 1,10,30 1,20, 1,43,110 1,74,18 1,88,112 and would like to create a 3d histogram data structure that i can use to create a 3d histogram or, more likely a heatmap. The unterlying data structure therefore needs to look like this: 0-10 11-20 21-30 31-40 0-10 11-20 21-30

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:

Hello, I have a large (919 X 919), hierarchically clustered heatmap that I would like to read the labels off of. I have tried saving the figure in pdf format and enlarging it until I can see the labels, but if I make the labels small enough to read (so that they don't overlap) using cexRow and cexCol, they do not appear in the pdf. The limit seems to be anything below cexRow or Col = 0.06.

I generated a heatmap in R using the following commands: > mydata <- read.csv(file="Data.csv", header=TRUE, sep=",") > mydata <- mydata[rowSums(mydata[,-1]^2) >0, ] > rownames(mydata)=mydata$Name > mydata <- mydata[,2:253] > mydatamatrix <- data.matrix(mydata) > mydatascale <- t(scale(t(mydatamatrix))) > hr <-

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

Hi R users, I'm a quite extensive user of the heatmap() function, and as many others i'm frequently frustrated by its fixed square width / height ratio. Here is a typical example : dev.new() heatmap(matrix(rnorm(1200), nrow=10)) I have a non square matrix to plot with heatmap, as there are many more columns than rows, row labels are larger than necessary but column labels

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 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, 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]),

I am using R version 2.12.1 on Win XP. I have done a heatmap with dendrogram using the heatmap.2 function. The heatmap basically looks like I want it to be, but the labels of the columns are cut off. I.e. the textual labels of the columns, although they are not very long (less than 12 characters), do not fit into the window and can not be read entirely. If I manually resize the graphics

Hello. I have following data: doze g1 g2 g3 g4 etc... 1200 a d 1100 b e 1158 c f 1500 a e 1403 c f ... etc. Doze - numeric, levels(g1)=c('a','b','c'), levels(g2)=c('d','e','f'). This is the data of genetic analysis, where the factors are genes and the numerical is some numerical value. I want to build up a function, which will do a preliminary

doh-trying again- this time remember text only. 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

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>