[BioC] Gating with an ellipsoidGate
jspidlen at bccrc.ca
Tue Sep 14 19:00:19 CEST 2010
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:
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.
> 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
> [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
> Many thanks for all your help,
> .''`. Roger Leigh
> : :' : Debian GNU/Linux http://people.debian.org/~rleigh/
> `. `' Printing on GNU/Linux? http://gutenprint.sourceforge.net/
> `- GPG Public Key: 0x25BFB848 Please GPG sign your mail.
More information about the Bioconductor