parseAnnotationXML: Recursively process an XML node for one FOV

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

Description

Visit each node in an object of class XMLNode and gather information to print one line for each vertex which represents the location of a cell on the slide [NOTE: DOUBLE CHECK THIS FOR ACCURACY]

Usage

parseAnnotationXML(node, fovName = NULL, outFile = NULL, LineColor = "",
  Name = "", Visible = "", RegionType = "", HasEndcaps = 0,
  NegativeROA = 0, boundaryColors = NULL)

Arguments

node	object of class XMLNode containing Halo annotations for one FOV
fovName	unique identifier of FOV
outFile	output file
LineColor	code for line color of the annotation ["655280"|"65535"|"255"]
Name	name of the annotation
Visible	logical indicating whether annotation is visible [????]
RegionType	region type *Note: any region with type other than Polygon is skipped
HasEndcaps	[???]
NegativeROA	[???]
boundaryColors	a list including hex colors for Tum, Exc, and Epi boundaries; default=list("65280"="Tum", "65535"="Exc", "255"="Epi")

Details

Output is a tab-delimited file containing: 1) FOV name 2) Annotation number 3) Line color 4) Name 5) Visible 6) Region number 7) Region type 8) HasEndcaps 9) NegativeROA 10) X coordinate 11) Y coordinate ***(negative of what is output by Halo)*** 12) Region according to color (Tumor, Exclusion, Epidermis)

Value

nothing

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