similar to: Assigning colors to cells

Hi all, I used image.plot() to create a heat map of a matrix: as.matrix(read.table("Matrix.txt", sep="\t"))->x HeatBrk<-seq(5,25,2.5) MyCol= gray((7:0)/7) library(fields) image.plot(x, col=MyCol, breaks=HeatBrk, legend.shrink=0.3) dev.copy(device=pdf, file="HEAT4!.pdf", height=8, width=8) dev.off() There are a few things that I would like to do that I

Hi all, I'm trying to build a package on Windows 7 (64 bit) and although R cmd build worked fine and I got pkg.tar.gz with no errors, but when I tried doing R CMD check everything turns out ok except for the warning: "checking whether package 'pkg' can be installed ... ERROR. Installation failed." It then refers me to the error file "00install.out" which reads as

All, I frequently make spreadsheets in Excel in which I rank values in columns by stop-light colors (red is bad, yellow is OK, green is good). Image and heatmap expect a matrix in which all the data are in the same scale, but I frequently have different scales in different columns. ie. Column one runs from 1-10 while column 2 runs from 1-100. I thus need to define a separate color ramp for each

Hello all, I used the following script to generate a plot, but when I try to place axes, the axes start at the end of my plot and continue off the plot; the attached image shows what happens when I try to generate axes. library(fields) as.matrix(read.table("Matrix.txt", sep="\t"))->x #the matrix is a square matrix measuring 104x104; it was too large to attach #on left:

> 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, 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

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, 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 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

Hi all: As to the "heatmap" function, the default style is "red and yellow",and red refers to low level and yellow refers to high level. How can I change the style to the contrary: red refers to high level and yellow refers to low level? Thanks a lot! My best [[alternative HTML version deleted]]

Dear R users, I am trying to print heatmaps in a loop (with a pause). Idea is to visualize changing correlations over time and for testing I wrote this simple (reproducible) code below. My problem is that levelplot() does not produce any output when I run the code (though heatmap does). Ideally I would like to use levelplot() as it produces a neat index on the side indicating the color and the

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 ==

Hi there, I'd like to create a heatmap from my matrix with a) a defined color range (lets say from yellow to red) b) using striking colors above and below a certain threshold (above = "green", below = "blue") Example matrix (there should be a few outliers generated...) + simple levelplot without outliers marked: library(lattice) my.mat <- matrix(rnorm(800), nrow =

Dear all, This seems like a simple problem but i've searched the help files and tried various options but failed, so apologies in advance for asking what i'm sure is an easy thing to do! In short, I have displayed behavioural data using the TraMineR package such that there is a colour change between the transition of behaviours, however, all the methods that i have used thus far have

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

Dear R-help, Could any of you direct me to a function for plotting a grid of colours, directly specified by a matrix of hex colour codes? In other words I'm looking for a heatmap() or image()-like function to which I can specify the colour of each grid location directly, rather than providing a numerical matrix and a 1D-colour scale (heatmap, image, levelplots,NeatMap...). I'm surprised

Hi, I have a matrix with both positive and negative numbers, I would like to use image() to draw a heatmap. How can I can design a palette (or is there a function already available) that treat negative numbers in a blue gradient and positive numbers in a red gradient and treat 0 as white? Thanks

My tuneR sawtooth wave function generator is broken. When I use the sine function, I get exactly what I expect: a sine wave whose frequency is defined by the freq parameter. In particular, higher frequencies have shorter wavelengths (more cycles per second means shorter waves). When I create a sawtooth wave, the opposite seems to occur: higher frequencies result in longer waves. But that?s not