getAllInfiltrationPlots: Create and store all infiltration plots in a list to be...

In caitlinjones/halo: Development version of the package 'halo', which analyzes and visualizes Halo data

Description

Create and store all infiltration plots in a list to be printed later

Usage

getAllInfiltrationPlots(den, bandWidth = NULL, config,
  yScaleConsistency = "population", absoluteDensity = TRUE,
  densityPercentage = TRUE, byFOV = TRUE, summarize = TRUE,
  stacked = TRUE, sampleOrder = NULL, infiltrationAreas = NULL,
  indivPopulations = TRUE, forceStack = FALSE)

Arguments

den	tibble with columns for Sample,SPOT,Band,Counts,Density
bandWidth	width of each band around tumor interface
config	parsed marker config (return value from getMarkerConfig())
yScaleConsistency	possible values: "population", "all", or "sample" indicating which subset of values to use to set maximum for all plots
absoluteDensity	logical indicating whether to plot density values on absolute scale (default=TRUE)
densityPercentage	logical indicating whether to plot density percentages (default=TRUE)
byFOV	logical indicating whether to generate plots for each individual FOV (default=TRUE)
summarize	logical indicating whether to generate summary plots of total band densities (ALL FOVs; default=TRUE)
stacked	logical indicating whether to generate plots of all cell types for a single marker set in a stacked bar chart (default=TRUE)
sampleOrder	vector of sample names in order they should appear on plots
infiltrationAreas	area data for each sample/spot/band
indivPopulations	plot populations individually; default=TRUE; if set to FALSE, ONLY stacked plots will be created

Value

list of all plots

caitlinjones/halo documentation built on May 7, 2019, 8 a.m.