markExclusions: Given a tibble of object analysis data, add a column EXCLUDE...

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

Description

Given a tibble of object analysis data, add a column EXCLUDE to indicate which cells should be excluded from further analysis, according to various upstream factors including drift/loss, border padding, and other technical reasons determined by investigators

Usage

markExclusions(samp, dat, drift, fovAnn, cellDiveId, haloAnn = NULL,
  borderPad = 20, driftThreshold = 0.1, printPlots = FALSE,
  debugDir = getwd(), boundaryColors = NULL,
  boundaryReassignmentFile = NULL)

Arguments

samp	sample name as it appears in both SampleAnnotations.xlsx and data
dat	tibble containing Halo object analysis data, to which EXCLUDE column will be added
drift	tibble of drift/loss summary
fovAnn	FOV annotations for one sample
cellDiveId	CELL_DIVE_ID mapping sample name to fov annotations
borderPad	number in pixels indicating the minimum distance between a cell and the FOV border in order for that cell NOT to be excluded
driftThreshold	maximum pixel percent determined to have drifted in order to NOT be excluded

Value

tibble matching dat exactly, with an extra column, EXCLUDE, added to indicate which cells should not be analyzed

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