VDJ_call_RECON: Calls the Kaplinsky/RECON tool

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Calls the Kaplinsky/RECON tool

Description

Calls the Kaplinsky/RECON tool on the VDJ/VDJ.GEX.matrix[[1]] object to infer the parent distribution of species and estimate their diversity. Outputs either a dataframe of the resulting means and weights of the RECON species parent distribution estimation or a plot of the original species distribution along resampled values from the reconstructed parent distribution.

Usage

VDJ_call_RECON(
  VDJ,
  recon.directory,
  feature.columns,
  grouping.column,
  VDJ.VJ.1chain,
  max.features,
  size.threshold,
  resample,
  max.feature.size,
  reticulate,
  operating.system
)

Arguments

VDJ	VDJ or VDJ.GEX.matrix[[1]] object, as obtained from the VDJ_GEX_matrix function in Platypus.
recon.directory	directory containing recon executable. Defaults to working directory/Recon
feature.columns	vector of strings/ string - columns denoting the unique species for RECON - e.g., could be the CDRH3s if feature.columns = 'VDJ_cdr3s_aa'. If more than one column is provided (e.g. c("VDJ_cdr3s_aa","VJ_cdr3s_aa")) these columns will be pasted together.
grouping.column	string - column determining the groups/ samples for the species observations. Defaults to 'sample_id' for per-repertoire analysis
VDJ.VJ.1chain	boolean, defaults to TRUE. Whether to filter out aberrant cells (more than 1 VDJ or VJ chain).
max.features	integer or 'all' - maximum number of features/species ot be considered for the RECON estimation. If 'all', will consider all species.
size.threshold	integer - the size threshold parameter for the RECON tool, as specified by the '-t' parameter.
resample	boolean - if T, will also perform and output a resample of the species frequencies/sizes from the inferred parent distribution.
max.feature.size	integer - the maximum size of species/features to be considered in the resulting plot (maximum number of elements on the x axis).
reticulate	boolean - if T, will create a new environment to install python and run the RECON tool, else, your environment must have a python version compatible with RECON installed.
operating.system	string - operating system on which RECON will be run. 'Windows' for Windows, 'Linux' for Linux, 'Darwin' for MacOS.

Value

The resulting means and weights of the RECON-inferred distribution as a seprate dataframe or appended to the VDJ, or a plot of resampled species sizes from the inferred distribution vs original sizes/frequencies.

Examples

## Not run: 
VDJ_call_RECON(VDJ, recon.directory='./Recon',
feature.columns = 'VDJ_cdr3s_aa', grouping.column = 'VDJ_cdr3s_aa')

## End(Not run)

Platypus documentation built on Aug. 15, 2022, 9:08 a.m.