[BioC] Overlay Density Plot for FlowSet

Florian Hahne fhahne at fhcrc.org
Fri Oct 10 07:03:50 CEST 2008

Hi Aric, sorry for the late reply, I didn't follow the mailing list  
the past several days.
Looks like a bug in flowViz on the Mac. Things are fine on my Linux  
box, but I get the same strange behavior on my Macbook.
There will be many changes and bug fixes with the upcoming release (in  
about two weeks, I think), and as far as I can tell right now this  
issue is already fixed in the latest devel version. There will also be  
significantly updated documentation and vignettes available, the  
current one is very slim, to put it nicely :)

I will check into this in more detail and get back to you tomorrow.  
Did the contour plot errors go away with the update? And what about  
the gate on the density plots? I am afraid I still don't get what the  
CD3.4.fp3Live.subset flowSet is. Is that the result of the subsetting  
operation using rectCCR7.filter? If that is the case you won't see the  
gate on the plot. We don't plot lines of gate boundaries on  
densityplots, but indicate the gate region by color shading. And if  
your plot the data after subsetting, the whole density region will be  
in the gate, hence the whole area will be shaded. It would be very  
helpful if you could send me a coherent piece of code that indicates  
what you try to do, ideally beginning at data import. It looks like  
you are only interested in two frames in the set, and sending either  
the two FCS files or a serialized version of CD3.4.fp3Livet[c(5,4)] to  
my FHCRC email address (fhahne add fhcrc dot org) would be very helpful.

On 06.10.2008, at 11:38, Aric Gregson wrote:

> Florian,
> On Fri, 03 Oct 2008 13:31:57 -0700
> Florian Hahne <fhahne at fhcrc.org> wrote:
>> Let me know if that doesn't address your problem. Also please provide
>> the output of sessionInfo() in future posts,
> I thought that perhaps the drawing of gates on the densityplot, the
> lack of contour() working and the fact that none of the gate outlines
> are ever drawn in xyplot(smooth=F) was due to my environment, so I
> upgraded. My machine environment is listed below. There was no change
> in plot results. I then tried on a clean install of R 2.7.2 and the
> most recent bioconductor packages (as of yesterday) for this version
> of R on a Mac (sessionInfo not listed) and there was no change in plot
> behavior.
> I used the same .RData and .Rhistory files on both machines, before
> and after the upgrades, if that makes a difference. I must be  
> setting up
> and adding gates incorrectly or something very odd is going on.
> I have also noticed that the following example from page 7 of
> 'filters.pdf' produces different results depending upon which version
> of the 'filters.pdf' document that I look at.
>> xyplot(`SSC-H` ~ `FSC-H` | Visit,
> +        data = transform("SSC-H"=asinh,"FSC-H"=asinh) %on% GvHD,
> +        subset = Patient == "6",
> +        filterResults = n2gate.results,
> +        filter = n2gate,
> +        smooth = FALSE, alpha = 0.1)
> In the filters.pdf dated March 21, 2008 the gated cells are pink and
> the gate is outlined (exactly what I cannot do), but in the June 3 and
> September 20 documents gated cells are black and there is not outline
> of the gate dimensions (which is what I am able to do). The example  
> that
> is supposed to draw a red outlined gate in xyplot(smooth =F) follows a
> similar pattern of color/no color. I have no problems getting a black
> outlined gate to be drawn on the plots with xyplot(smooth=T).
> Any further suggestions would be greatly appreciated.
> thanks!
>> sessionInfo()
> R version 2.7.0 (2008-04-22)
> i386-pc-solaris2.11
> locale:
> C
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets   
> methods
> [8] base
> other attached packages:
> [1] flowViz_1.4.1      latticeExtra_0.5-2 lattice_0.17-15
> RColorBrewer_1.0-2 [5] flowCore_1.6.0     Biobase_2.0.1
> feature_1.1-13     KernSmooth_2.22-22 [9] rrcov_0.4-07
> robustbase_0.4-3
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.2.2 DBI_0.2-4           MASS_7.2-44
> [4] RSQLite_0.7-0       geneplotter_1.18.0  grid_2.7.0
> [7] stats4_2.7.0
> aric
> -- 
> Aric Gregson <a.gregson at ucla.edu>

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