cell2: Function to run CellID

In gerbeldo/tidycell: CellID Data Analysis Inside the Tidyverse

Function to run CellID

Description

Function to run CellID

Usage

cell2(
  arguments,
  cell.command = NULL,
  no_cores = NULL,
  debug_flag = 0,
  dry = F,
  encode_cellID_in_pixels = F,
  fill_interior_pixels = F,
  label_cells_in_bf = F,
  output_coords_to_tsv = F,
  ignore.stdout = T,
  intern = T
)

Arguments

arguments	An argument data.frame, as built by rcell2::cellArgs2.
cell.command	Path to the binary executable (get if from https://github.com/darksideoftheshmoo/cellID-linux). Or "cellBUILTIN" for the builtin binary.
no_cores	Position-wise parallelization,internally capped to number of positions in cell.args.
debug_flag	Set to 0 to disable CellID printf messages (builtin CellID only).
dry	Do everything without actually running CellID, print the commands that would have been issued.
encode_cellID_in_pixels	Set to TRUE to write cell interior and boundary pixels with intensity-encoded CellIDs and blank the rest of the image (CellID option '-s').
fill_interior_pixels	Set to TRUE to fill each cell interior area in the output image file with intensity-labeled pixels (CellID option '-i').
label_cells_in_bf	Set to TRUE to enable labeling of cells with their CellID in the BF output image (CellID option '-l', default FALSE).
output_coords_to_tsv	Set to TRUE to write cell interior and boundary pixels data to a .tsv file in the output directory (CellID option '-m').
ignore.stdout	Set to FALSE to see CellID output from a system call.
intern	Set to TRUE to save CellID output from a system call to a file in the "out" directories (one per position) and the commands to a file at the first "path" in the arguments data.frame.

Value

A dataframe with one column indicating the issued commands. Use rcell2::load_cell_data to get the results from the CellID output, typically located at the images path.

gerbeldo/tidycell documentation built on Aug. 15, 2022, 2:35 p.m.