[BioC] flowCore gate syntax

[Byron Ellis]

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
>
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-- 
Byron Ellis (byron.ellis at gmail.com)
"Oook" -- The Librarian