printInfiltrationDensityPlots: Print density plots

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

Description

Print density plots

Usage

printInfiltrationDensityPlots(den, bandWidth = NULL, config,
  yScaleConsistency = "population", indivPopulations = TRUE,
  absoluteDensity = TRUE, densityPercentage = TRUE, byFOV = TRUE,
  summarize = TRUE, stacked = TRUE, forceStack = FALSE,
  sampleOrder = NULL, separateLegend = TRUE, infiltrationAreas = NULL,
  outDir = NULL, sampleSummaryRows = NULL, sampleSummaryCols = NULL,
  sampleSummaryPtsPerPage = NULL)

Arguments

den	tibble containing densities for all markers to be plotted
bandWidth	if plotting by distance intervals from infiltration boundary, this is the size of each interval
config	tibble containing marker configureation (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
byFOV	logical; print plots of each FOV (all FOV on one panel); 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
sampleSummaryRows	number of rows to include on each page of sample summary file; default=NULL
sampleSummaryCols	number of cols to include on each page of sample summary file; default=NULL
sampleSummaryPtsPerPage	number of patients to include on each page of sample summary file; can be used instead of sampleSummary[Rows|Cols]; default=NULL
areaDat	tibble containing area data for all Samples, FOVs and Bands

Value

nothing

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