similar to: heatmap.2 clustering and adding add.expr

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>

Hello, I'm new to R and have been following many guides including the two-way anova (http://www.personality-project.org/r/r.anova.html). Using that walkthrough including the supplied data I do str(data.ex2) and receive the appropriate types of data as follows: > str(data.ex2) 'data.frame': 16 obs. of 4 variables: $ Observation: int 1 2 3 4 5 6 7 8 9 10 ... $ Gender :

Full_Name: Kevin R. Coombes Version: 2.1.0 OS: Windows XP Submission from: (NULL) (143.111.224.169) When revC = TRUE and RowSideColors is set to a list of colors in heatmap, then the image and dendrogram are inverted, but the row-side color map does not change. The following script illustrates the problem. ############## set.seed(1023) # generate columns of two different types d1 <-

Thanks Tom. heatmap.2(mat, Rowv=NA, Colv=NA, col=redgreen, breaks=seq(-1,1,by=0.01), symm=TRUE, trace="none", dendrogram="none") that did the trick :) Begin forwarded message: From: "Leja, Thomas" Date: 29 March 2011 03:47:59 GMT+01:00 To: "Benton, Paul" Subject: Re: [R] comparing heatmaps Yep, you have to specify the range for colours. I usually

Problem on flexmix when trying to apply signature developed in one model to a new sample. Dear R Users, R Core Team, I have a problem when trying to know the classification of the tested cases using two variables with the function of flexmix: After importing the database and creating a matrix: BM<-cbind(Data$var1,Data$var2) I see that the best model has 2 groups and use: ex2

When investigating the legend(x,y, expression ( <math>, <math> ), ....) [as suggested by Jim Lindsey], I once again stumbled over the fact that expression objects behave somewhat ``wierdly'', IMHO. We can have expressions of length(.) > 1, and access elements of these like list elements. However, other natural things don't work with expressions; some example

Hi all, I tried testing with Rspec for first time, following a tutorial. "rspec spec/" works fine but when I try ''autotest'' it gives me the error message below. I also made a gist about it: https://gist.github.com/779265 It seems like a redgreen or ZenTest error. I''m using Ubuntu10, Rails3, Ruby 1.9 and RVM. Any help is appriciated, thanks in advance, gezope

Dear r heper, How can I change the strip text, for example (16,23] in the following example, to other more informative text such as "high level" on the fly? library(effects) Cowles$ex2 <- cut(Cowles$extraversion,3) mod.cowles <- glm(volunteer ~ sex+neuroticism*ex2,data=Cowles, family=binomial) eff.cowles <- allEffects(mod.cowles) plot(eff.cowles,

Hello all, I am using the heatmap.2 function in the gplots package. I want to supress the reordering of the columns of the data matrix i pass to the function. I used the statement, heatmap.2(z,Colv=FALSE,dendrogram="row",col=redgreen(75)) where z, is the matrix of data. The output i want should have the rows reordered along with the dendrogram and the columns should be in the original

Dear all, I've been trying to find how to compare tow different heatmaps but I'm having trouble getting the colors bar to be the same. I'm doing something like the following: library(gplots) dat<-cor(matrix(rnorm(100, m=10), nrow=10)) mat<-cor(matrix(rnorm(100), nrow=10)) dev.new() heatmap.2(mat, Rowv=NA, Colv=NA, col=redgreen(75), symm=TRUE, trace="none",

Hi everyone, I am beginner using R but I try to learn more. I need this graphic or similar but instead of tropical and temperate are three ontogenetic states Larva Met Juv CTMAX CTMIN SP SP SP This is my scrip: Ex = subset(Expr, Outlayer=="N") Ex2 = subset (Ex, S0 == 1) Ex3

Here are my patches to add extra shapes to the annotate plugin. I have also added dbus support and made a few things configurable. The new tools available are Line, Rectangle and Circle, the original is called Brush. There is no selection line at the moment because I do not understand OpenGL yet. Hopefully these patches can be added and something added later. There is an extra action called

Hi there, I checked google for aov. usually one uses summary to see whether the p-value is small. but I want to put aov in my script. how can I get the p-value, (0.1115, 0.6665, 0.6665 in the following example)? thanks YU > datafilename="http://personality-project.org/r/datasets/R.appendix2.data" > data.example2=read.table(datafilename,header=T) > aov.ex2 =

On Jan 20, 2008 7:52 PM, G-man <gregor007 at gmail.com> wrote: > I''ve set up my tests, and when I run the whole thing, I get this for my > views: > > 3) > NoMethodError in ''/chapters/new.html.erb should render new form'' > undefined method `process_clean_up_fixtures'' for >

Hello, I am trying to create a heatmap that clusters based on a k-means scheme rather than a hierarchical clustering scheme. Suppose I have the following input data, located in sample.table: x1 x2 x3 x4 x1 17.198 16.306 16.806 16.374 x2 14.554 10.866 15.780 14.596 x3 14.374 14.118 14.569 17.352 x4 17.505 14.596 15.738 14.070 By using the heatmap.2 function as follows, I can create a heatmap

I've got two tables.... first one(table1): ID chrom start end Ex1 2 152 180 Ex2 10 2000 2220 Ex3 15 3000 4000 second one ( table2): chrom location name 2 160 Alv 2 190 GNN 2 100

Full_Name: Karsten Krug Version: 2.4.0 OS: Open Suse 10.0, Windows XP Submission from: (NULL) (88.134.13.50) I found a problem in the 'optimise' function for one dimensional optimisation. Example 1: Try to find a maximum of the function below with the use of 'optimise' in the interval [0,0.5]. The function follows a parabola and has two local maxima located at the margins of

Hi, i have a network with one machine acting as master router with 2x4-Port-Ethernet-Cards in it - running nmbd! There are two Windows-Workgroups, WRK1 and WRK2 in each there are Windows-Exchange-Servers EX1, EX2. In WRK2 the PDC is on EX2, in WRK1 there is a standalone PDC, PDC1. Every network is a full 255 IP-Network. 192.168.40.1 WRK1 EX1 (192.168.40.40) PDC1 (192.168.40.42) 192.168.41.1

Hello all, I''m new to rSpec but after reading a couple of tutorials I''ve become enamored. Anyway, I am at minute 42 of the rSpec basics screencast ( peepcode.com) and I''m having the following error running autotest w/rSpec: D:\ruby\projects\forecaster>autotest loading autotest/rails_rspec c:\ruby\bin\ruby -rrubygems -e "require ''redgreen''"

I had an error message while running a macro from Yudi Pawitan's web site: > source("ex2-13.r") Error in parse(file, n, text, prompt) : syntax error on line 2 Inspecting ex2-13.r I found that the error was generated by another source() command. Clearly R does not like nested source()s, which is fair enough when you think about it. Still it's something that you might want