fs.plot: Plot of Functionality Score vs some other axis

In seshadrilab/COMPASSHelpers: Collection of helper functions for analyzing FCM data

Description

TODO: Make another function for paired values (i.e. line plot)

Usage

fs.plot(compassResultOrPath, stratifyBy, ylims = NULL, outdir = NULL,
  plotTextExtra = "", plotWilcox = FALSE, themeBaseSize = 18,
  removeGridAndBg = FALSE, showTitle = TRUE,
  showSignificanceBracket = TRUE, gsOrGsListOrPath = NULL,
  polyfunctionality = F, pvalue_fontsize = NULL,
  axestitle_fontsize = NULL, axestick_fontsize = NULL, font = NULL,
  geom_jitter_width = 0.15, xaxis_title = stratifyBy)

Arguments

compassResultOrPath	the COMPASSResult object or path to a COMPASSResult RDS object on disk
stratifyBy	Character vector of metadata columns to stratify plot by
outdir	If given, plot will be saved to this directory instead of being returned in a list along with plot data
plotTextExtra	Extra text (e.g. "CD4+, Peptide Pool 1") to place in plot title and filename. Commas and spaces, etc will be removed for filename.
gsOrGsListOrPath	(optional) Either a GatingSet, a GatingSetList, or path to one of these objects on disk. You can specify this if you want to use its metadata instead of the metadata in the COMPASSResult object
polyfunctionality	Display Polyfunctionality Score instead of Functionality Score

Examples

## Not run: 
fsPlotList <- fs.plot(gsOrGsListOrPath="path/to/GatingSet/Folder",
       compassResultOrPath="path/to/CompassResultRDSFile.rds",
       stratifyBy="DiseaseState",
       plotTextExtra="",
       plotWilcox=TRUE)

## End(Not run)

seshadrilab/COMPASSHelpers documentation built on May 6, 2019, 6:04 p.m.