printTotalFOVDensityPlots: Print plots of total FOV marker density plots

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

Description

Print plots of total FOV marker density plots

Usage

printTotalFOVDensityPlots(den, fovAreas, config,
  yScaleConsistency = "population", indivPopulations = TRUE,
  absoluteDensity = TRUE, densityPercentage = TRUE, summarize = TRUE,
  stacked = TRUE, forceStack = FALSE, sampleOrder = NULL, outDir = NULL,
  annotationCols = NULL)

Arguments

den	tibble containing densities for all markers to be plotted
fovAreas	tibble containing area data for all Samples and FOVs
config	tibble containing marker configuration (returned from getMarkerConfig())
yScaleConsistency	level on which y-scales should be the same; choices: ["byPopulation"|"all"|"markerSet"]
indivPopulations	logical; print a plot for each individual population; default=TRUE
absoluteDensity	logical; print plots of absolute density values; default=TRUE
densityPercentage	logical; print plots of density percentage values; default=TRUE
summarize	logical; print summary plots, showing density of ALL FOV together; default=TRUE
stacked	logical; for plots with all exclusive markers, print stacked bar plots; default=TRUE
forceStack	force stacking of cell types even if they appear to be unstackable
sampleOrder	vector of samples in order that they should appear on plot
outDir	directory where all plots will be printed, organized by marker set
annotationCols	vector of column names to use for annotation

Value

nothing

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