Cloud Plotting? flowViz/Core
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Aric Gregson ▴ 270
@aric-gregson-3058
Last seen 7.7 years ago
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? 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. 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 -- Aric Gregson <a.gregson at="" ucla.edu="">
flowViz flowViz • 766 views
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Florian Hahne ▴ 540
@florian-hahne-2471
Last seen 7.7 years ago
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)? Florian > 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 206-667-3148 fhahne at fhcrc.org
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Florian, --On March 6, 2009 2:02:30 PM -0800 Florian Hahne <fhahne at="" fhcrc.org=""> wrote: >> 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? >> > 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. Yes, I actually meant to say 3D cloud. I don't think that cloud itself would be very useful. Aric
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