[BioC] Place summary stats in names in flowViz xyplot

Florian Hahne fhahne at fhcrc.org
Fri Mar 20 03:01:57 CET 2009

Hi Aric,
you have to adapt the panel function to make this happen. Start by  
taking a look at panel.xyplot.flowframe in the flowViz package. Seems  
like all you need to do is add an appropriate names argument to the  
call to glpolygon. The modified panel function has then to be supplied  
to the xyplot function via the panel argument.
An even cleaner solution would be to have your panel function call the  
predefined flowVIz one without plotting the gates, and then adding  
gates including the names in a second step. Deepayan's lattice book  
available from Springer is an excellent source to learn more about the  
concept of lattice and the panel function.

On 18.03.2009, at 19:36, Aric Gregson wrote:

> Hello,
> I'm trying to get the summary stats, such as the percent positive
> events, to be drawn onto the xyplot in place of the gate name. I can
> get this to work fine with the following code for a single file, but I
> am having trouble getting the results for the entire flowSet to be
> printed.
> xyplot(`APC.H7.A` ~ `Pacific.Blue.A`,
> 	Data(wf[["agate"]]),
>       filter=afilter,
>       smooth=F,
>       alpha=0.5,
>       pch=21,
>       cex=0.4,
> ->    subset = Filename == 327,
>       scales=list(tick.number=10),
>       outline=TRUE,
> ->    names = format(summary(wf[["anothergate"]])$percent
> 		[[4]], digits =3),
>       par.settings=list(gate=list(col="purple", alpha=.3),
>         gate.text=list(col="black", alpha=0.7, cex=0.6)))
> Removing subset and attempting to get all of the stats placed causes
> only the first value of the flowSet summary result to be placed in all
> plots. For example,
>> summary(wf[["anothergate"]])$percent
> [1] 28.940568  5.272565  8.464079 46.257443 28.265877
> When plotted only 28.9 is placed in all plots. I have tried many
> variations, including trying to make it a factor and plotting the
> levels, but then of course it only plots the first ordered level in  
> all
> plots.
> Any suggestions would be greatly appreciated.
> Thanks, Aric
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