search for: redgreen

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 ------ Error message: <internal:lib/rubygems/custom_require>:29:in `require'': no such file to load -- test/unit/ui/console/testrunner (LoadError) from <i...

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 order without any dendrogram. For the above statement i am getting an error: Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim...

I''ve made a model called Color to manage custom styles for my application. It works find when I''m running it locally in Mongrel, and I haven''t tried to deploy it yet. I use ZenTest and Autotest, and when I run autotest I''m getting the following message: "C:/rails/band/trunk/app/models/color.rb:1: Color is not a class (TypeError)" My Color model is

...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''" -S script/spec -O spec/spec.opts spec/models/weather_spec.rb spec/views/weathers/show.rhtml_spec.rb spec/controllers/weathers_controller_spec.rb spec/views/weathers/new.rhtml_spec.rb spec/views/weathers/edit.rhtml_spec.rb spec/helpers/weathers_helper_spec.rb spec/views/weathers/in...

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 spe...

...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", dendrogram="none", main = paste("Correlation Matrix for time delay at ", sep="")) dev.new() heatmap.2(dat, Rowv=NA, Colv=NA, col=redgreen(75), symm=TRUE, trace="none", dendrogram="none", main = paste...

...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 using hierarchical clustering: library(gplots) x=read.table('sample.table', header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=redgreen(75), trace="none") However, I am now interested in trying to show a heatmap in which the data is clustered using k-means. By looking at some previous posts on the mailing lists, and the documentation, I've attempted to cluster my data using kmeans using the following modified script:...

...e? > Also, no word on my autotest question? > > c:\rails\rails_apps\tracker>autotest > loading autotest/rails_rspec > from > C:\Rails\rails_apps\tracker\vendor\plugins\rspec_on_rails\lib\autotest\rails_rspec.rb > C:\Rails\ruby\bin\ruby -rrubygems -e "require ''redgreen''" -S script/spec > -O spec/spec.opts spec/controllers/chapters_routing_spec.rb > invalid option: -O > Test::Unit automatic runner. > Usage: -e [options] [-- untouched arguments] There was another thread about this just a day or two ago. Not sure what exactly the probl...

...fMat,border){ cAbove = expand.grid(1:nx,1:ny)[tfMat,] xl=cAbove[,1]-0.49 yb=cAbove[,2]-0.49 xr=cAbove[,1]+0.49 yt=cAbove[,2]+0.49 rect(xl,yb,xr,yt,border=border,lwd=3) } ###heatmap without reordering ############## heatmap.2(ex2$cor,Colv=FALSE,dendrogram="none",Rowv=FALSE,col=redgreen(25), density.info ="none",trace="none",add.expr={makeRects(sig,"orange")},revC=TRUE) I want to create a heatmap with clustering and reordering but my sig matrix is according to unordered matrix . I tried usings cluster1<-hclust(dist(d874n)) cluster1$order The r...

...ese microRNA. So, like: cell1 cell2 miRNA1 1.5 3.4 miRNA2 1.3 2.4 ................... miRNA50 5 2.1 miRNA51 7.3 0.5 I want to see some miRNA are high in cell1 and low in cell2 but others are low in cell1 and high in cell2. I use heatmap.2(dataset, col=redgreen(50), scale="row"). But I can only see two colors represent high and low values. Actually, i want to see there are color variation in high values area too(rather than just one color in high value area and one color in low value area). You know what I mean? I know I have two columns so the...

Has anyone else encountered this problem? What I mean is, rspec_autotest runs all specs, then waits. When you change a spec, it reruns that spec. However, if that spec now passes, it should run the whole suite again, so you can see the next one to work on. It no longer does this. This renders it somewhat useless. Does anyone have autotest working with rspec 0.7.5, or does anyone have any

...quot;shoulda", :git => "git://github.com/thoughtbot/shoulda.git" gem ''factory_girl_rails'' gem ''cucumber'' end gem "devise", :git => "git://github.com/plataformatec/devise.git" gem ''cancan'' gem ''redgreen'' gem ''formtastic'', :git => "git://github.com/justinfrench/ formtastic.git", :branch => "rails3" gem ''mail'' After installing all the gems and running rspec ./spec/controllers/ some_file.rb I get the following error: http://gist...

In case anyone else is trying to make this work, here is what I did (Before 0.7.4 I had patched the regex in zentest redgreen, but that is not used any more) To use directly, it is very simple. In rspec_autotest/lib/ rspec_autotest.rb, add a -c to the spec_command in the initializer function: @spec_command = "spec -c --diff unified" This won''t help however if you want to use rails_spec_server....

RSpec-1.1.3 has been released. If you''re using RSpec and autotest, you''ll have to upgrade to RSpec-1.1.3 and ZenTest-3.9.0 at the same time. == Version 1.1.3 Maintenance release. * Tightened up exceptions list in autotest/rails_spec. Closes #264. * Applied patch from Ryan Davis for ZenTest-3.9.0 compatibility * Applied patch from Kero to add step_upcoming to story listeners.

I'm using this code to create a heatmap of expression data and indicate a specific column of data, post clustering: #Generate heatmap: heatmapChipDx <- heatmap.2(L3data_med2, dendrogram="column",trace="none", col=redgreen(64), colsep=seps, sepcolor="yellow", sepwidth = 0.1, margin=c(5,5), scale="row", key=FALSE) I have two problems that I'm hoping i can get some pointers on: 1. The column I want to indicate with a yellow line is column #1 in the matrix, pre-clustering. How can I determine i...

Hi, I hope to show a heatmap with thre colours, no gradation. How to specify heatmap.2 to map "green" for values less than -1, "gray" for values between -1 and 1, and "red" for values greater than 1 ? Thanks [[alternative HTML version deleted]]

I managed to have Autotest running on my windows box. Apparently all is working but every time I know there is an error a new line is generated, no error messages or anything is sent to the console. I am using pastie now (thanks to David), please go to: http://pastie.caboo.se/106155 Daniel -- Posted via http://www.ruby-forum.com/.

I'm working on some heatmaps, and the person I'm working with would prefer a red-black-green color palette (red denoting gene induction and green denoting gene repression). Does such a palette exist already? If not, is there an easy way to create one? Thanks, Jake

...se gem ''letter_opener'' end group :production do # Use unicorn as the web server # gem ''unicorn'' end group :development, :test do gem ''brakeman'' gem ''shoulda'' gem ''shoulda-matchers'' gem ''redgreen'' gem ''diff-lcs'' gem ''cucumber-rails'' gem ''capybara'' gem ''database_cleaner'' gem ''rspec-rails'', ''2.7.0'' gem ''rspec_tag_matchers'' gem ''factor...

Hey, I''m trying to configure autotest with rspec on cygwin but something is going wrong. I made a very simple testing environment with a user.rb and user_spec.rb file. Rspec works fine, but autotest outputs nothing - it just stays here, idle. ^C doesn''t display anything more. I can see it''s running because I added require ''autotest/snarl'' in my