Question: FlowViz and FlowStats Interaction in Gates on densityplots
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gravatar for Aric Gregson
5.3 years ago by
Aric Gregson50
Aric Gregson50 wrote:
Hello, I am again running through some older code with flowViz and flowStats in R and finding new incompatibilities. I have also found some very nice enhancements. :) I have very many rangeGate objects from flowStats that I had been using to plot gates on densityplots from flowViz. This worked like a charm previously. Now however, it seems that densityplot complains when one of the values is NA, NaN or Inf. Of course, rangeGate creates values that often (always?) include 'Inf'. The workaround is to create a manual gate that does not have 'Inf' as the higher end on the gate, but clearly that negates the entire reason for using reproducible code and R. Example code as below. filter_range_exosome <- rangeGate(Data(wf[['rect_bead+']]), stain="FL2.H", filterId="Exosomes", plot=FALSE, sd=0.1 ) densityplot(NAME ~ ., Data(wf[['rect_bead+']]), par.strip.text=list(cex=0.7), channels="FL2.H", main="Exosome Population", filter=filter_range_exosome, alpha=0.4, xlab="CD9-PE", groups=TYPE, fitGate=TRUE ) Produces the following notice in the plot: 'Error using packet 1 'to' cannot be Na, NaN or infinite.' I'm am certainly missing something, perhaps a new function for developing a rangeGate that works with densityplot? If needed I can create some reproducible example with the GvH data, but I think this is clear enough to get it started. Thanks very much, Aric
flowviz flowstats • 624 views
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