plotFACSArrangedEgs: Arrange Example FACS Plots in stacks of Two

In NKInstinct/manuscriptIL23R: Plotting and tumor-handling functions for the IL23R Manuscript/Project

Description

This function creates the stacked example plots used throughout the manuscript. Generally, these compare one WT and one IL23RKO example, but it is extensible to other grids (such as the 2x2 used in the antibody graphs) by simply passing a longer list of GatingHierarchies. By default, this also applies biex scaling to both axes, and does NOT currently support modifying their params from the default, so if that becomes important later I'll need to add it in.

Usage

plotFACSArrangedEgs(
  egList,
  x,
  y,
  gate,
  ...,
  ncol = 1,
  xlim = c(-500, 20000),
  ylim = c(-500, 20000),
  biexTrans = "both"
)

Arguments

egList	List of GatingHierarchies to plot in order given (so start with WT!)
x	String specifying x-axis parameter, as either channel or marker name
y	String specifying y-axis parameter, as either channel or marker name
gate	String specifying gate or gates (as character vector in that case)
...	Additional args to pass to plotFACSExample
ncol	Numeric specifying the number of expected columns in the arranged output
xlim	Length-two numeric vector giving coord_cartesian the x-axis limits
ylim	Length-two numeric vector giving coord_cartesian the y-axis limits
biexTrans	String specifying whether a flowjo-style biex transform should be applied to "both" (default), "x", or "y" axes. Any other input results in no transform.

Value

A ggarrange'd collection of ggplot objects

NKInstinct/manuscriptIL23R documentation built on Jan. 1, 2022, 1 p.m.