similar to: Half of a heatmap

> I am trying to produce a heatmap of pairwise correlations, but since the matrix is > symmetric, I only need either the upper or the lower triangle. I have scoured the > web and R documentation, but I have not been able to find a way to produce such a > figure. Is there a simple way to produce a heat map with only the part above or > below the diagonal? You might want to check

Hi , I am trying to plot a heatmap with a correlation matrix and trying to highlight significant correlations . i am using my matrix d874n has 78 columns ex2<-corAndPvalue(data.matrix(d874n),use = "pairwise.complete.obs") ##creating a matrix of true false using p values sig<-ex2$p<0.05 nx=78 ny=78 makeRects <- function(tfMat,border){ cAbove =

Hi, I am having troubles with heatmap(). I have a matrix containing pairwise distance values and I want to plot this matrix with heatmap. I wonder now what distfun is for. Is a distance matrix computed from my initial matrix again and then plotted? cheers, andreas

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

Dear list members, I have been using R to create a heatmap where my data has continous variables from 0 to 100. When I create the heatmap, although the branches are correct, they do not order themselves so that the row with the most zeros is at one end and the row with the most 100s is at the other, which is what I would like them to do, so as to create a colour gradient down the graphic. I have

Hey, I am still working on my heat map (for those who are read my previous post about row.names)… Now, I would like to save my heat map.2 in .png or .tiff in order being able to work on the picture in photoshop, but it doesn't work. I'am using (as I have found on some forum) > png("heatmap.2.png) # and it just doesn't work. when I try doing it with::

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

I am making heatmaps for a dataset (~ 300*600 matrix) with the following R script (I am not familiar with R and this is the first time I am using it). library("gplots") library("Cairo") mydata <- read.csv(file="data.csv", header=TRUE, sep=",") rownames(mydata)=mydata$Name mydata <- mydata[,2:297] mydatamatrix <- data.matrix(mydata) mydatascale

Esteemed R-users, heatmap.2() is yielding an inappropriate key based on my colors and break-points. In the reproducible example below, the key is inappropriate (to me) because- 1. 'Orange' is simply not represented in the key, despite its prescence in the heatmap. 2. The proportions of the key are clearly out, ie., my largest bin, (0.1 - 0.2) is half the range, but this bin (colored

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

Hi! I'm displaying a contingency table with heatmap(): > svm.predPix.tabla svm.predPix CC DD LL NN NN2 CC 22 0 3 8 3 DD 0 27 0 1 0 LL 1 1 90 3 7 NN 2 0 1 11 4 NN2 0 0 5 1 20 > heatmap(svm.predPix.tabla[5:1,], Rowv=NA, Colv=NA,col = rev(heat.colors(32)), scale="column", margins=c(5,10)) and I'm happy

Hi there! I'm having some strange permissions issues with one of my systems that's on an Active Directory domain. Here's the basic background: - System is joined to AD domain. Users authenticate fine via Kerberos, and are authorized via an AD user group. They can browse the share, create files, etc. without incident. "valid users" lets them in. - User information for the

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

Hello All, I have a simple question based on how things are labeled on my heat map; particularly, there is this annoying "X" that appears before the numeric value of all the labels of my columns. Let's say I have the following silly data, stored in "temp.txt" 1905 1910 1950 1992 2011 2020 Gnat 0.08 0.29 0.29 0.37 0.39 0.43 Snake

I have a huge dataset(15k X 18) and tried to use the heatmap in R to examine the patterns. However, I found that heatmap and heatmap.2 gave me completely different outputs. Here are the codes: ------------ > dim(as.matrix(data.dcpm)) [1] 15462??? 18 > > heatmap(as.matrix(data.dcpm), col=topo.colors(100)) > heatmap.2(as.matrix(data.dcpm), col=topo.colors(100), key=TRUE,

Hi, I am trying to create a heatmap with some specific requirements. Specifically, I need to be able to center the color-scale around 0, and I need to truncate the data so that a few extreme values do not cause the rest of the heatmap to appear black (on a red/green scale). After reading through and experimenting with heatmap, heatmap.2, heatmap_plus, and heatmap_2, I believe heatmap.2 will

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),

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 all, I'm trying to use heat.map to display some data. The data is originally in csv format and when I read it in R using read.table I get: a b c d e 1 A 1 1 1 1 2 B 1 0 1 1 3 C 0 1 0 1 4 D 1 1 1 0 5 E 1 0 0 0 The problem is, that for heatmap I need a numerical matrix. When using data.matrix I get: a b c d e [1,] 1 1 1 1 1 [2,] 2 1 0 1 1 [3,] 3 0 1 0 1 [4,] 4 1 1 1 0 [5,] 5 1 0 0 0 So

Can someone recommend a more sophisticated way to annotate heatmaps than the ColSideColors argument of heatmap and heatmap.2? In particular, I would like to be able to annotate columns with more than one piece of information, like in Figure 1 of the article at http://www3.interscience.wiley.com/cgi-bin/fulltext/117905619/HTMLSTART / doi:10.1002/hep.22256. Some example data and a heatmap: