flowViz xyplot smooth=F gate outline ONLY
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Aric Gregson ▴ 270
@aric-gregson-3058
Last seen 9.6 years ago
--On June 26, 2009 2:40:58 PM -0700 Deepayan Sarkar <deepayan.sarkar at="" gmail.com=""> wrote: > On Wed, Jun 24, 2009 at 4:15 PM, Aric Gregson<a.gregson at="" ucla.edu=""> wrote: [snip] >> >> 1) ONLY outline the gated cells rather than color and outline the >> cells. I have not found a way to do this. The best I have managed is in >> the example below, which overdraws with a light rose color. Setting >> fill = "transparent" appears to have no effect. >> >> 2) Apply this type of plot to a flowSet. I have not figured this out >> yet either. Replacing panel.xyplot.flowframe with panel.xyplot.flowset >> fails. > > Looks like you are calling panel.xyplot.flowframe() only to draw the > gate. That's not necessary; you can call glpolygon() directly. For > example, > > library(flowViz) > data(GvHD) > > my.panel <- function(x, y, ..., frame, my.filter) > { > cols <- > densCols(x, y, nbin=128, > colramp = colorRampPalette(rainbow(7))) > panel.xyplot(x, y, col = cols, ...) > glpolygon(filter(frame, my.filter)) > } [snip] This works beautifully. Thank you. > The details may need to be tweaked depending on your filter. This is > harder to generalize for flowSets so that all kinds of filters are > handled, but specific types are simple: > > xyplot(`FSC-H` ~ `SSC-H`, GvHD[1:4], > my.filter = norm2Filter("SSC-H", "FSC-H"), > pch = 21, cex = 0.3, > panel = function(x, frames, channel.x, channel.y, ...) { > nm <- as.character(x) > x <- flowViz:::evalInFlowFrame(channel.x, frames[[nm]]) > y <- flowViz:::evalInFlowFrame(channel.y, frames[[nm]]) > my.panel(x, y, frame = frames[[nm]], ...) > }) This also works very well so far. Thank you very much. I never would have figured out this syntax. Sorry for the delay in responding, but I had to update R, there seems to be trouble with the densCols function in earlier versions. Thanks again! Aric
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