plotMarkerPercentages: Make a grid of pie charts, one for each given marker showing...

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

Description

Make a grid of pie charts, one for each given marker showing the percentages of all the marker combinations in which that positive marker is included

Usage

plotMarkerPercentages(countsTable, markerNames, type = "bar",
  other_threshold = 0.05, exclude_sample_fov = NULL, pdfFile = NULL,
  custom_colors = FALSE)

Arguments

countsTable	tibble of counts generated by countMarkers()
markerNames	vector of positive markers, for each of which a pie will be made
type	type of chart ["bar"|"pie"]; default="bar"
other_threshold	all markers making up less that this percentage will be put togther in a marker combination named 'other'; default=0.05
exclude_sample_fov	a string of Sample FOVs to exclude from analysis in the form: 'Sample1:2+4+3,Sample2:1,Sample3:2+4'
pdfFile	output PDF file
custom_colors	use color scheme defined in getMarkerColors(); TO DO: CHANGE THIS

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