similar to: Brewer.pal error

Hi, I have been trying to plot density plots using the example on: http://addictedtor.free.fr/graphiques/graphcode.php?graph=139 I used to use this function, but I cannot get any old code or even the example to work. library("geneplotter") require("RColorBrewer") x1 <- matrix(rnorm(1e4), ncol=2) x2 <- matrix(rnorm(1e4, mean=3, sd=1.5), ncol=2) x <-

Anyone who is interested in using optimal colour palettes should look at the work of Cindy Brewer: www.colorbrewer.org I have written code to use her colour schemes in R. It is included below. Perhaps someone may find this interesting enough to work into a package. Included also is a function showpalette, which was posted here a while back. I don't remember who wrote it. I have copied all

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 <-

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 <-

Estimado Jose: En nuestro caso utilizamos las mismas librerias y solemos resolverlo asi (donde el color depende del valor que se le asigne) //-------------------------------------------------------------------------------------------------------------------------------------- #configuramos donde setwd("D:/mapas/") #Carga de librerias library (sp) library (RColorBrewer) library

Dear all, Considering this simple example of hexbinplot: mixdata <- data.frame(x = c(rnorm(5000), rnorm(5000,4,1.5)), y = c(rnorm(5000), rnorm(5000,2,3)), a = gl(2, 5000)) fig <- hexbinplot(y ~ x | a, mixdata) print(fig) update(fig, colramp = BTC) produces a bad (non-updated) legend. Compare it with: hexbinplot(y ~ x | a, mixdata, colramp = BTC) What

Hi everybody, just arrived at R and immediately I got a problem. Here's my script: setwd("C:/Users/Tom/Eigene Tools/Programming/R/Data") blast_hits<-read.table("blastHit_covLenght.txt", header=T) blast_hits <- as.matrix(blast_hits) numerical1<-data.matrix(blast_hits, rownames.force = NA)

I'm looking for a scheme to generate a default color palette for plotting points, lines and text (on a white or transparent background) with from 2 to say 9 colors with the following constraints: - "red" is reserved for another purpose - colors should be highly distinct - avoid light colors (like "yellow"s) In RColorBrewer, most of the schemes are designed for area fill

Hello, Is there a simple way to get the class type for each column of a data.frame? I am in the situation where I would like to get all the columns of a data.frame that are factors. I have tried: apply(df,2,class) but all the columns come back as class "character". Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of

Hello, I would like to reshape my data for presentation purposes from something like this: > test <- data.frame(a=c("A","A","A","A","B","B","B"),b=c(1,1,2,2,1,1,1),c=1:7) > test a b c 1 A 1 1 2 A 1 2 3 A 2 3 4 A 2 4 5 B 1 5 6 B 1 6 7 B 1 7 to something like this: a b c 1 A 1 1,2 3 A 2 3,4 5 B 1 5,6,7 This seems

Simple question how can you position text in the top left hand corner of a plot? I am plotting multiple plots using par(mfrow=c(2,3)) and all I want to do is label these plots a), b), c) etc. I have been fiddling around with both text and mtext but without much luck. text is fine but each plot has a different scale on the axis and so this makes it problematic. What is the best way to do this?

Hi, I was just wondering if anyone had created a 64 bit binary for SUSE 10.1 x86_64 yet. Unfortunately, I upgraded before looking whether a package was available and now cannot find a suitable package on CRAN. If noone has produced one yet, does anyone have any idea when one will be available? Many Thanks Daniel Brewer

Hi, I'm trying to draw a 2D plot using multiple tints of red. The (simplified) setup is the following: || year | x | y || My idea is that each year is plotted with a different tint of red. Older year (lightest) -> Later year (darkest). I've managed to plot this with different scales of grays simply by doing: palette(gray(length(years):0/length(years))) before the plot and for each

Hi, I have a particular barplot I would like to generate, but I am having trouble getting it to work. What I would like is in effect two barplots with stacked bars merged into one. For example, I have two samples (yoda1,yoda2) on which I measure whether two variables (var1,var2) are present or absent for a number of measurements on that sample. > var1 <- data.frame(yoda1=c(3,7),

Hi. I'm admin at a computer lab. Just started here, and I'm trying to set samba up. I'm having the following problem: The server (FreeBSD 4.7) has a HP LaserJet 6MP installed on it. So far so good, works great. When installing this printer on network computers, I have no problem, even printing, but someone installed the wrong driver (fortunatelly its a PS driver). When I try to

Does anyone have any ideas how I could do a power calculation for a log rank test. I would like to know what the suggested sample sizes would be to pick a difference when the control to active are in a ratio of 80% to 20%. Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Email: daniel.brewer at icr.ac.uk

Hello, I would like to calculate the 95% confidence intervals for the estimates of a linear model and I just wanted to check that I am doing it correct. Is it just: Estimate + 1.95996*Std.Error to Estimate - 1.95996*Std.Error or is there another approach that doesn't assume a normal distrbution? Thanks. Apologies for my naiivity Dan --

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 >

I am trying to create a map with selected states based on highest to lowest mean cost. The following code properly selects the correct states, and the legend is properly color coded with ranges, but the colors per range does not match the state colors. I need help getting the state colors to match the ranges outlined in the legend. I have tried ordering the mean amounts and this correctly creates

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When