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Question: densityplot in flowViz
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gravatar for Jiang, Mike
3.2 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:
 

Thanks, Mike, that did the trick! John

> On Jul 29, 2015, at 8:34 PM, Jiang, Mike <wjiang2@scharp.org> 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 <wjiang2@scharp.org> 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
>> 

ADD COMMENTlink written 3.2 years ago by Jiang, Mike1.2k
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