[BioC] Gating with an ellipsoidGate

[Josef Spidlen]

Hi Roger,
I am not the author of flowCore but I believe the ellipsoid gate 
constructor takes covariance matrices since this is used in the 
Gating-ML specification. Mathematically, this is a nice way to specify 
ellipsoids in multidimensional space.

I have posted a simple spreadsheet that allows you to convert the 
representation of an ellipse by half-axes, rotation and centre point to 
covariance matrix, mean (= centre point), and distance square (=1 for 
this case). Please follow this link for download:
http://sourceforge.net/projects/flowcyt/files/Gating-ML/Gating-ML%201.5/EllipseCalculations.xls/download
I hope this addresses your issues; let me know if further help is needed.

Unfortunately, I'll have to leave it up to the flowCore/flowViz authors 
to get back to you with your other questions.

Cheers,
Josef

> Message: 6
> Date: Mon, 13 Sep 2010 15:51:55 +0100
> From: Roger Leigh<rleigh at codelibre.net>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] FlowCore/FlowViz issues
> Message-ID:<20100913145155.GW6128 at codelibre.net>
> Content-Type: text/plain; charset=utf-8
>
> Hi,
>
> [Apologies if this is delivered twice; my initial mail didn't
> appear to be accepted for several hours, and I didn't see any
> failure message; does the list object to GPG signatures?]
>
> I've just started to use FlowCore/FlowViz to analyse some of my
> flow cytometry data, and ran into a few problems.  I'm hoping
> that you might be able to point me in the right direction!
>
> I've been very pleased with it so far, and have got some nice
> plots and stats out of it, but I'm sure I'm doing some things
> very inefficiently and/or incorrectly!
>
> [I'm using R version 2.11.1 (2010-05-31) on x86_64-pc-linux-gnu
> (Debian GNU/Linux) with current Bioconductor packages)]
>
>
> 1) Gating with an ellipsoidGate
>
> cov<- matrix(c(400000000, 0, 0, 0.08), ncol=2,
>                dimnames=list(c("FS.Lin", "SS.Log"), c("FS.Lin", "SS.Log")))
> mean<- c("FS.Lin"=32000, "SS.Log"=2.8)
> cells<- ellipsoidGate(filterId="CellGate", .gate=cov, mean=mean)
>
> I want to select my cells using an ellipsoid gate on forward- and side-
> scatter plots.  In the above situation, they lie in a region where
> FS=32000?10000 and log??(SS)=2.8?0.5.  However, the values in the
> covariance matrix don't match the dimensions; is there any explanation
> regarding how to construct a covariance matrix from the actual
> dimension I want (I got the above by trial and error until it fitted
> nicely--I'm afraid I know little about these matrices).
>
> In some plots I'd also like to rotate the ellipse, but I'm not sure
> how to put this into the matrix, if that's the way to do things.
> Is this possible?
>
> Is there an alternative constructor to create a gate from real
> dimensions?
>
>
>
> Many thanks for all your help,
> Roger
>
> --
>    .''`.  Roger Leigh
>   : :' :  Debian GNU/Linux             http://people.debian.org/~rleigh/
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>