Hi R-Users,
I posted this question a while ago on the bioconductor mailing list but got no
answers. Maybe here is somebody who might know a solution:
I failed at drawing multiple filters in a densityplot() using the
FlowCore/FlowViz packages.
I
found a way to draw multiple filters in xyplot(), using the glpolygon
method within the panel-function, but some similar attempts for
densityplot failed.
I could draw simply some vertical lines using
panel.abline, but this doesn't look as appealing as the original method
when using a single filter with the standard filter=xyz argument.
I
bet there is a method to draw multiple gates through the panel-function,
as curv1filter can also identify multiple peaks automatically and
draw them into a densityplot...
This script works for xyplot but not for densitylot:
library(flowCore)
library(flowViz)
data(GvHD)
Filter1 <- rectangleGate(filterId="Filter1",
"FSC-H" = c(0, 200))
Filter2 <- rectangleGate(filterId="Filter1",
"FSC-H" = c(300, 400))
xyplot( `SSC-H` ~ `FSC-H` , data=GvHD[[1]],
panel = function(...) {
panel.xyplot.flowset(...)
glpolygon( Filter1 )
glpolygon( Filter2 )
}
)
densityplot( ~ `FSC-H`, data=GvHD[[1]],
panel = function(...) {
panel.densityplot.flowset(...)
glpolygon( Filter1 )
glpolygon( Filter2 )
}
)
The glpolygon method yields not the "typical" look of the densityplot
filters, but red lined gate boundaries. The desired look of the filter is a
lighter color and dotted lines as limits.
Thank you in advance!
All the best,
Michael
--
Michael Jahn
PhD student
Helmholtz-Centre for Environmental Research
Leipzig, Germany
http://www.ufz.de(http://www.ufz.de/)
(http://www.ufz.de/)
[[alternative HTML version deleted]]
