plotCellTypeLocations: Plot location of given cell types within one FOV

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

Description

Given a halo data *.rda file with XML annotations and a list of cell types, plot the X and Y coordinates of those cells showing locations relative to each other and to tissue boundary

Usage

plotCellTypeLocations(dataFiles, annotationsDirs, cellTypesFile, boundaryColors,
  cellTypeColors, pad = 30, pdfFile = NULL)

Arguments

dataFiles	*.rda file containing ObjectAnalysisData
annotationsDirs	directory of *.annotations XML files from Halo for one sample
cellTypesFile	text file containing a list of cell type markers, one on each line; each cell type marker may consist of an indivdual marker or a comma-
boundaryColors	a list of hexadecimal color codes for Tum, Exc, and Epi boundaries
cellTypeColors	a list of hexadecimal color codes for each cell type in cellTypesFile
pad	amount to trim from each FOV
pdfFile	name of output PDF file

Value

nothing

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