generate.pxp.image.data: Used to create the pixel-by-pixel graph data and return a...
In AstroPathJHU/mIFTO: mIFTO: Multiplex Immunoflourescence Titration Optimization

generate.pxp.image.data

R Documentation

Used to create the pixel-by-pixel graph data and return a table; Created By: Benjamin Green; Last Edited 08/11/2020

Description

This function is desgined to do analysis for IF titration series in Pixel by Pixel data provding output for each IMAGE individually grouped by Concentration

Usage

generate.pxp.image.data(
  Concentration,
  x,
  y,
  q,
  Antibody_Opal,
  titration.type.name,
  Thresholds,
  paths,
  connected.pixels,
  flowout,
  Opal1,
  decile.logical,
  threshold.logical
)

Arguments

`Concentration`	a numeric vector of concentrations used in the titration
`x`	a unique identifier for the slide to be analyzed
`y`	the numeric of which index from the concentration vector to use
`q`	the image coordinates of the current image as a comma separated pair
`Antibody_Opal`	the paired string for an antibody opal pair, designated as "AB (Opal NNN)"
`titration.type.name`	the type of titration that was performed (TSA or Primary)
`Thresholds`	a list of thresholds used for each concentration and slide
`paths`	the paths to the data as a list, with an element for each concentration
`connected.pixels`	the number of pixels that a pixel must be connected to for positivity measures
`flowout`	logical for whether or not flow like results will be produced
`Opal1`	the opal value of interest
`decile.logical`	whether or not to run a decile approach analysis
`threshold.logical`	whether or not to run a threshold approach analysis