co_agg: 3D co-aggregation
In Russel88/RCon3D: Analysis of Confocal Images of Microbial Biofilms

co_agg

R Documentation

3D co-aggregation

Description

Function to calculate the pairwise 3D co-aggregation between two channels

Usage

co_agg(
  imgs,
  channels,
  size,
  npixel,
  R = 10,
  dstep = 1,
  pwidth,
  zstep,
  cores = 1,
  kern.smooth = NULL,
  layers = NULL,
  naming = NULL
)

co_agg.default(
  imgs,
  channels,
  size,
  npixel,
  dstep = 1,
  pwidth,
  zstep,
  cores = 1,
  kern.smooth = NULL,
  layers = NULL,
  naming = NULL
)

Arguments

`imgs`	The paths of array files; i.e. output from `loadIMG` or `findIMG` functions.
`channels`	Character vector with names of the two channels to calculate co-aggregation for. Should be in the names of the array files
`size`	The maximum distance (microns) to examine. Has to be a multiple of both pwidth and zstep. Beware, increasing size will increase runtime exponetially!
`npixel`	Number of random pixels to examine. Increasing this will increase precision (and runtime in a linear fashion)
`R`	Number of times to run the co-aggregation analysis
`dstep`	The interval between examined distances (microns). Increasing this decreases resolution but speeds up function linearly. Defaults to 1
`pwidth`	Width of pixels in microns
`zstep`	z-step in microns
`cores`	The number of cores to use. Defaults to 1
`kern.smooth`	Optional. Numeric vector indicating range of median smoothing in the x,y,z directions. Has to be odd intergers. c(1,1,1) means no smoothing.
`layers`	Optional. Should the function only look in a subset of layers. A list with lists of layers to use for each image. Can also be the output from `extract_layers`
`naming`	Optional. Add metadata to the output dataframe by looking through names of array files. Should be a list of character vectors, each list element will be added as a variable. Example: naming=list(Time=c("T0","T1","T2")). The function inserts a variable called Time, and then looks through the names of the array files and inserts characters mathcing either T0, T1 or T2