arguments: Obtener argumentos para CellID

In gerbeldo/rcell2: CellID Data Analysis Inside the Tidyverse

Obtener argumentos para CellID

Description

Obtener argumentos para CellID

Usage

arguments(
  path,
  parameters = rcell2::parameters.write(),
  BF.pattern = "^BF",
  file.pattern = "^(BF|[A-Z]FP)_Position(\\d+)_time(\\d+).tif$",
  file.pattern.groups.order = c("ch", "pos", "t.frame"),
  tiff.ext = "tif$"
)

Arguments

path	directory where images are stored, full path.
parameters	path to the parameters file or a data.frame with "pos" (position number) and "parameter" (path) columns. Defaults to parameters.write().
BF.pattern	regex pattern to detect BF images only. Defaults to: "^BF"
file.pattern	regex pattern for all tif files, with one group for each of c("ch", "pos", "t.frame") in file.pattern.groups.order. Uses "^(BF|[A-Z]FP)_Position(\d+)_time(\d+).tif$" by default. To omit time, use an empty group for the t.frame in the regex, for example: "^(BF|[A-Z]FP)_Position(\d+)().tif$".
file.pattern.groups.order	a character vector of components c("ch", "z", "pos", "t.frame") with order corresponding to the order of groups in file.pattern.
tiff.ext	regex pattern for the tif file extension

Details

All 4 regex groups are mandatory, 't.frame' may be left as empty parenthesis, while also preserving group order defined by 'file.pattern.groups.order'.

The "channel" and "pos" regex groups _must always_ match pos and channel identifiers in the file name.

Example 'file.pattern' regex, when 'file.pattern.groups.order = c("ch", "pos", "t.frame")':

With Z planes time: file.pattern = "^(BF|[TYR]FP|[TYR]\d{2})_Position(\d+)_time(\d+).tif$"

No Z planes, with time (note the empty parentheses): file.pattern = "^(BF|[A-Z]FP)_Position(\d+)_time(\d+).tif$"

No Z planes, no time: file.pattern = "^(BF|[TYR]FP)_Position(\d+)().tif$"

Value

a data.frame with all the information needed to run CellID

gerbeldo/rcell2 documentation built on Aug. 15, 2022, 7:20 a.m.