Hi, I am not sure if this is the proper way to ask questions about flowCore. If it's not, please excuse me. I've noticed that it has several gates (rectangleGate, polygonGate, polytopeGate and ellipsoidGate) but only rectangleGate syntax is covered in the documentation (it was written April 25, 2007) where can I find the proper syntax for each of these gates? by the way, congratulations for this excellent contribution for everyone that works with flow cytometry thanks in advance Leonardo Kenji Shikida

Hello, the syntax for the rectangleGate, polygonGate and polytopeGate is identical (except for a bug in polygonGate, which we'll get to in a second), which is why they all point to the same manpage. The idea is that there are two basic ways people will want to do things. First, someone at the command line or a script creating a gate directly. Here, we want to support "direct assignment" so: rectangleGate("myGate","FSC-A"=c(10,50),"SSC-A"=c(30,40)) polygonGate("myGate2","FSC-A"=c(10,20,30),"SSC-A"=c(15,25,35)) Unfortunately, due to a bug in polygonGate this second one doesn't work! Fortunately, it was an easy bug to fix so I'll check it in for a bugfix release. The other mode (and the one that works for polygon gates) is a programmatic mode where we create matrix with columns being parameters, the idea being that this is easier to create within functions: polygonGate("myGate3",cbind("FSC-A"=c(10,20,30),"SSC-A"=c(15,25,35))) which creates the same gate using a matrix. You can see this in the examples as well. On 4/26/07, Leonardo Kenji Shikida <shikida at="" gmail.com=""> wrote: > Hi, I am not sure if this is the proper way to ask questions about > flowCore. If it's not, please excuse me. > > I've noticed that it has several gates (rectangleGate, polygonGate, > polytopeGate and ellipsoidGate) but only rectangleGate syntax is > covered in the documentation (it was written April 25, 2007) > > where can I find the proper syntax for each of these gates? > > by the way, congratulations for this excellent contribution for > everyone that works with flow cytometry > > thanks in advance > > Leonardo Kenji Shikida > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Byron Ellis (byron.ellis at gmail.com) "Oook" -- The Librarian