[BioC] Cloud Plotting? flowViz/Core

Florian Hahne fhahne at fhcrc.org
Fri Mar 6 23:02:30 CET 2009

Aric Gregson wrote:
> Hello, 
> There does not appear to be any implementation of the corresponding
> cloud plot from lattice in flowViz, is that correct? Would it be
> possible or is it planned to implement it? 
Hi Aric,
at the moment there are no concrete plans of doing so. However, you are 
invited to try an implementation yourself. All that needs to be done is 
to write an S4 method for flowFrames and flowSets, and it might be as 
simple as extracting the data and faking the necessary formula to plot 
the right parameters. However, I expect this to be very slow because 
typical flow data sets are too big to efficiently plot individual 
points, and a 3D density representation might be more useful.
> Also, this may be a sort of bug, not sure. Not a big deal, as no one
> uses plot(), but still this does not follow the most recent flowCore
> pamphlet.
Yikes. Used to work before but I assume that either changes in the name 
space or the methods package broke it. It is sort of non-standard use of 
S4 methods, so maybe somebody else could help out here. The issue is 
that we define an S4 method in flowCore that tells people to attach 
flowViz. In flowViz we define another plot method with exactly the same 
signature which does the plotting, and the idea was that this method now 
overwrites the flowCore one. Is there a way to force the calling of a 
method from a particular package (or rather name space)?

> plot(Data(wf[["asinh"]]),"SSC.A")
> For plotting, please attach the 'flowViz' package.
>    i.e., 'library(flowViz)'
>> sessionInfo()
> R version 2.8.0 (2008-10-20) 
> i386-pc-solaris2.11 
> locale:
> C
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets
> methods [8] base     
> other attached packages:
> [1] flowViz_1.7.10   lattice_0.17-15  flowCore_1.9.18  rrcov_0.4-07    
> [5] robustbase_0.4-3 Biobase_2.2.1   
> loaded via a namespace (and not attached):
>  [1] AnnotationDbi_1.4.1 DBI_0.2-4           KernSmooth_2.22-22 
>  [4] MASS_7.2-44         RColorBrewer_1.0-2  RSQLite_0.7-1      
>  [7] cluster_1.11.11     feature_1.1-14      geneplotter_1.20.0 
> [10] graph_1.20.0        grid_2.8.0          latticeExtra_0.5-4 
> [13] stats4_2.8.0        tcltk_2.8.0        
> Thanks, 
> Aric

Florian Hahne, PhD
Computational Biology Program
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
fhahne at fhcrc.org

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