[BioC] FlowViz xyplot event limit

[Finak, Greg]

Hi, Roger

Subsampling your data for plotting runs the risk of losing details in rwgioms of low density (i.e. rare events). Another option would be to use contour plots of the density estimate (if I recall correctly, flowViz does support this) or simply pass smooth=TRUE.

Best,
Greg

Sent from my iPhone

On 2011-03-01, at 7:46 AM, "Davide Rambaldi" <davide.rambaldi at ifom-ieo-campus.it> wrote:

> I am still practicing with flowCore, but what about this?:
> 
> lines <- sample(100:500, 50)
> y <- read.FCS(file.name, which.lines=sample)
> 
> regards
> Davide
> 
> 
> On Mar 1, 2011, at 4:34 PM, Roger Leigh wrote:
> 
>> Hi,
>> 
>> I'm using xyplot with smooth=FALSE, outline=TRUE to get a plain
>> dotplot.  Unfortunately, some of my data has a great deal of
>> events (~5×10⁴), and even after gating the number of dots is too
>> great.  Details are lost, and the size of the PDF output is huge.
>> 
>> What I'd like to do is restrict the plot to a certain number of
>> events e.g. 1×10⁴.  This doesn't appear to be directly possible
>> with xyplot.  Can a flowFrame be trimmed down to a certain number
>> of events, such as the first 1×10⁴?  Due to gating, I can't gate on
>> the event count because this won't give me /n/ events because the
>> numbers aren't continuous.
>> 
>> 
>> Many thanks,
>> Roger Leigh
>> 
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> 
> Davide Rambaldi, Bioinformatics PostDoc.
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