map.and.plot.threshold.graphs: Used by PxP script to write out the threshold type graphs
In AstroPathJHU/mIFTO: mIFTO: Multiplex Immunoflourescence Titration Optimization

map.and.plot.threshold.graphs

R Documentation

Used by PxP script to write out the threshold type graphs

Description

Created By: Benjamin Green Last Edited 07/30/2020

Usage

map.and.plot.threshold.graphs(
  wd,
  Antibody_Opal,
  Antibody,
  Slide_Descript,
  Concentration,
  Tables,
  Thresholds,
  connected.pixels,
  ihc.logical,
  ihc.Thresholds,
  ihc.connected.pixels,
  folders.px,
  theme1,
  con_type,
  colors,
  Antibody_Opal.snratio,
  Antibody_Opal.ttest,
  pb.Object
)

Arguments

`wd`	the main data root directory
`Antibody_Opal`	the paired string for an antibody opal pair, designated as "AB (Opal NNN)"
`Antibody`	the string for an antibody
`Concentration`	a numeric vector of concentrations used in the titration
`Tables`	the table of statistics gathered by PxP
`Thresholds`	a list of thresholds used for each concentration and slide
`connected.pixels`	the number of pixels that a pixel must be connected to for positivity measures
`ihc.logical`	whether or not an IHC was done on these slides
`ihc.Thresholds`	a list of thresholds used for each slide for the IHC, should be in the same order as the slide list
`ihc.connected.pixels`	a list of conn pixels used for each slide for the IHC, should be in the same order as the slide list
`folders.px`	whether or not tiffs are divided into a number of folders or not
`theme1`	graphing theme
`con_type`	the type of concentration vector to use factor or numeric
`colors`	the color vectors for the t test and histograms
`Antibody_Opal.snratio`	Antibody Opal string for sn ratio graphs
`Antibody_Opal.ttest`	Antibody Opal string for ttest graphs
`pb.Object`	progress bar object
`Slide_Desctipt`	a unique identifier for each slide to be analyzed