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Question: densityplot in flowViz
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3.1 years ago by
Jiang, Mike1.1k
 Thanks, Mike, that did the trick! John > On Jul 29, 2015, at 8:34 PM, Jiang, Mike wrote: >  > sorry, It is the 'name' column of pData that should be updated. e.g. > pData(fs)[["name"]] <- c("s1", "s2") >  > Mike > ________________________________________ > From: John DeFilippo [defilippo.john@gmail.com] > Sent: Monday, July 27, 2015 11:19 AM > To: Jiang, Mike > Subject: Re: densityplot() >  > Hi Mike, >  >> There is currently no way to change the y axis label. You will have to name each sample within flowSet properly (using 'sampleNames(fs) <- newNames') before pass it to densityplot. >  >  > I renamed the flowFrames of my flowSet (see code below) prior to plotting with densityplot(), but my y-axis labels are still ‘V1’, ‘V2’, and ‘V3’. > Any further suggestions as to how I can get the new flowFrame names to show on the y-axis? >  >> trans.fs > A flowSet with 3 experiments. > sampleNames(trans.fs) <- c('Diadema', 'Lacunter', 'Tripneustes') >> trans.fs[[1]] > flowFrame object 'Diadema' >> trans.fs[[2]] > flowFrame object 'Lacunter' >> trans.fs[[3]] > flowFrame object ‘Tripneustes' >  > Thanks, >  > John >  >> On Jul 26, 2015, at 7:12 PM, Jiang, Mike wrote: >>  >> 'curv1Filter' is a special filter that generates a 'multipleFilterResult' instead of a regular 'logicalFilterResult' (from 'rectangleGate' or 'polygonGate'). So 'flowViz' has some difficulty to determine which population to select for computing statistics. >> For one dimensional gating, we find ourselves barely use 'curv1Filter', instead "openCyto::mindensity" is mostly useful. So I'd recommend you try that if there is no compelling reason to stick to 'curv1Filter'. >>  >> Do be able to set xlim, you will have to do densityplot on one channel at a time. >>  >> There is currently no way to change the y axis label. You will have to name each sample within flowSet properly (using 'sampleNames(fs) <- newNames') before pass it to densityplot. >>  >> Mike >> ________________________________________ >> From: John DeFilippo [defilippo.john@gmail.com] >> Sent: Sunday, July 26, 2015 2:28 PM >> To: Jiang, Mike >> Subject: densityplot() >>  >> Hi Mike, >>  >> I’m a biologist, not a biostatistician or computer scientist, so I apologize ahead of time for my ignorance. >>  >> I’m trying to do stacked 1D densityplot()s of several flowFrames in a flowSet, with gates and their percentages. >>  >> I can do 1D stacked densityplot()s of multiple channels with gates via: >>  >>> densityplot(~, trans.fs, channels = c('EV', 'SS', 'FL1', 'FL2'), filter = list(curv1Filter('EV'), curv1Filter('SS'), curv1Filter('FL1'), curv1Filter('FL2')), xlab = 'V1=Diadema, V2=, Lacunter, V3=Tripneustes’) >>  >> But as soon as I try to add statistics, even of just a single channel, >>  >>> densityplot(~ EV, trans.fs, filter=curv1Filter("EV"), fitGate=FALSE, stats=TRUE) >>  >> I’ll only get a plot of the last flowFrame in the flowSet, with neither gates nor statistics, and an error message: >>  >> ‘Error using packet 1, Unable to convert to a logical vector’ >>  >> How can I get percentages to show? >>  >> Also, if I’m doing multiple channels in the same densityplot(), is there a way to set xlim() for one or more channels (they would not have the same xlim). >>  >> And finally, is there a way to change the flowFrame labels in the y-axis? Each flowFrame was created by pooling all the flowFrames in a flowSet, so ended up as ‘anonymous’. Then I put them into a vector and coerced it into a flowSet so I could stack the plots, but the new flowFrames in the flowSet have the vector names v1, v2, v3, which is what displays on the y-axis. I’d like to customize their names. >>  >> Thank you for any help you can provide. The gate statistics is really my most important need. >>  >> Regards, >>  >> John DeFilippo >>