plotExclusions: Plot cell locations of exclusions

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

Description

Plot cell locations of exclusions

Usage

plotExclusions(dd, haloAnnotations = NULL, iFiles = NULL, aFiles = NULL,
  epFiles = NULL, gFiles = NULL, outDir = getwd(),
  boundaryColors = NULL, boundaryReassignmentFile = NULL)

Arguments

dd	data for one sample with EXCLUDE column
haloAnnotations	halo annotations in list format, for one sample and one or multiple FOV
iFiles	if not providing haloAnnotations, a vector of interface XML files
aFiles	if not providing haloAnnotations, a vector of exclusion XML files
epFiles	if not providing haloAnnotations, a vector of epidermis XML files
gFiles	if not providing haloAnnotations, a vector of glass XML files
outDir	directory where plots should be saved
boundaryColors	list of boundary colors as they appear in halo annotation XML files where the values are the associated boundary code (e.g., 'epiB', 'glsB', etc.)
boundaryReassignmentFile	comma-separated file indicating exceptions to the color assignments in boundaryColors

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