boxplot.cell.counts: Plot cell counts for each sample (default CD3+ cells)
In seshadrilab/flowHelpers: Collection of helper functions for analyzing FCM data

Description Usage Arguments Value Examples

Plot the number of cells that are CD3+ (or your specified population) for each sample. Run this function once for each batch to be combined later. Can use to look for batch effects.

boxplot.cell.counts <- function(flowJoXmlPath=NULL, gatingSetPath=NULL,
                    fcsPath=if (!.isnull(flowJoXmlPath)) { dirname(flowJoXmlPath) },
                    outdir=NULL, sampleGroup=3, subpopulation="3+",
                    keywords2import=NULL, stratifyByLevel1, stratifyByLevel2=NULL)

`flowJoXmlPath`	full path to FlowJo Xml file for import (flowJoXmlPath or gatingSetPath or gatingSet is required)
`gatingSetPath`	path to saved GatingSet directory for import (flowJoXmlPath or gatingSetPath or gatingSet is required)
`gatingSet`	a GatingSet object (flowJoXmlPath or gatingSetPath or gatingSet is required)]
`fcsPath`	(Optional) directory where FCS files reside, if not in the same directory as flowJoXmlPath
`outdir`	(Optional) directory to save boxplot in. If not given, returns the boxplot instead.
`sampleGroup`	(Optional) Specify this if you are providing a flowJoXmlPath and the flowJo sample group is not 3
`subpopulation`	(Optional) node name to use for counts, if not 3+
`keywords2import`	(Optional) keywords to import from flowJo into GatingSet metadata, required for flowJoXmlPath
`stratifyByLevel1`	Required keyword on which to stratify boxplot data (usually "PATIENT ID")
`stratifyByLevel2`	(Optional) additional keyword on which to stratify boxplot data
`batch`	the batch name, required if data is passed in as a gatingSet
`threshold`	(Optional) where to draw the threshold cutoff line for number of cells, default 25,000
`yUpperExpand`	(Optional) This will expand the yaxis to have this upper limit, if applicable.

Boxplot of cell counts stratified by stratifyByLevel1, unless outdir is specified.

## Not run: 
boxplot.cell.counts(flowJoXmlPath="/home/Batch1Directory/Batch1FlowJo.xml",
                    keywords2import=c("PATIENT ID", "Barcode"),
                    stratifyByLevel1="PATIENT ID",
                    stratifyByLevel2="Barcode")
                    
## End(Not run)