getAllTotalFOVPlots: 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

getAllTotalFOVPlots(den, config, indivPopulations = TRUE,
  absoluteDensity = TRUE, densityPercentage = TRUE, summarize = TRUE,
  stacked = TRUE, fovAreas = NULL, forceStack = FALSE, yMax = NULL,
  annotationCols = NULL)

Arguments

den	tibble with columns for Sample,SPOT,Band,Counts,Density
config	parsed marker config (return value from getMarkerConfig())
indivPopulations	plot populations individually; default=TRUE; if set to FALSE, ONLY stacked plots will be created
absoluteDensity	logical indicating whether to plot density values on absolute scale (default=TRUE)
densityPercentage	logical indicating whether to plot density percentages (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)
fovAreas	area data for each sample/spot
forceStack	force stacking of cell types even if they appear to be unstackable
yMax	maximum y value for all plots
annotationCols	vector of column names to use for annotation
sampleOrder	vector of sample names in order they should appear on plots

Value

list of all plots

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