data_add_pops: Add Population to IFC_data Object

In IFC: Tools for Imaging Flow Cytometry

Add Population to IFC_data Object

Description

Adds populations to an already existing 'IFC_data' object.

Usage

data_add_pops(
  obj,
  pops,
  pnt_in_poly_algorithm = 1,
  pnt_in_poly_epsilon = 1e-12,
  display_progress = TRUE,
  ...
)

Arguments

obj	an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).
pops	a list of population(s) to add to 'obj'. Each element of this list will be coerced by buildPopulation.
pnt_in_poly_algorithm	algorithm used to determine if object belongs to a polygon region or not. Default is 1. Note that for the moment only 1(Trigonometry) is available.
pnt_in_poly_epsilon	epsilon to determine if object belongs to a polygon region or not. It only applies when algorithm is 1. Default is 1e-12.
display_progress	whether to display a progress bar. Default is TRUE.
...	Other arguments to be passed.

Details

A warning will be thrown if a provided population is already existing in 'obj'.
In such a case this population will not be added to 'obj'.
If any input population is not well defined and can't be created then an error will occur.

Value

an IFC_data object with pops added.

Source

For pnt_in_poly_algorithm, Trigonometry, is an adaptation of Jeremy VanDerWal's code https://github.com/jjvanderwal/SDMTools

Examples

if(requireNamespace("IFCdata", quietly = TRUE)) {
  ## use a daf file
  file_daf <- system.file("extdata", "example.daf", package = "IFCdata")
  daf <- ExtractFromDAF(fileName = file_daf)
  ## copy 1st population from existing daf
  pop <- daf$pops[[1]]
  if(length(pop) != 0) {
    pop_copy <- pop
    ## modify name, obj and type of copied population
    pop_copy$name <- paste0(pop_copy$name,"_copy")
    pop_copy$obj <- (which(pop_copy$obj)-1)[1]
    pop_copy$type <- "T"
    ## create new object with this new population
    dafnew <- data_add_pops(obj = daf, pops = list(pop_copy))
  }
} else {
  message(sprintf('Please run `install.packages("IFCdata", repos = "%s", type = "source")` %s',
                  'https://gitdemont.github.io/IFCdata/',
                  'to install extra files required to run this example.'))
}

IFC documentation built on Sept. 14, 2023, 1:08 a.m.