makeSampleInfiltrationDensityPlots: Generate all infiltration density plots for a single sample

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

Description

Generate all infiltration density plots for a single sample

Usage

makeSampleInfiltrationDensityPlots(den, config, markers, bandWidth,
  sampleOrder = NULL, plotTitle = NULL, yMax = NULL, sumYmax = NULL,
  byFOV = TRUE, absoluteDensity = TRUE, densityPercentage = TRUE,
  summarize = TRUE, summaryTitle = NULL, forceStack = FALSE)

Arguments

den	tibble with columns for Sample,SPOT,Band,Counts,Density
config	parsed marker config (return value from getMarkerConfig())
markers	vector of marker combinations to plot
bandWidth	width of each band around tumor interface
sampleOrder	vector of sample names in order they should appear on plots
plotTitle	title to appear on plot
yMax	maximum y value for all plots
byFOV	logical indicating whether to generate plots for each individual FOV (default=TRUE)
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)
summaryTitle	title to appear on summary plots
stacked	logical indicating whether to generate plots of all cell types for a single marker set in a stacked bar chart (default=TRUE)

Value

list of sample plots

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