annotate: Add plate and well metadata.

In cytomining/cytotools: Command-Line Tools to Get Things Done Using Cytominer

Description

annotate adds plate and well metadata, as well as optional external metadata. It assumes the following files exist:

• <workspace_dir>/metadata/<batch_id>/barcode_platemap.csv which maps the plate barcodes to the corresponding platemaps,

• For each platemap, a file <workspace_dir>/metadata/<batch_id>/platemap/<plate_map_name>.txt which contains the metadata for each well position

Additional metadata can be appended to the output file via the optional external_metadata parameter. external_metadata is a CSV file. The following columns are required:

• Metadata_Plate

• Metadata_Well

The Metadata_ prefix can be dropped from required columns if the remaining metadata columns aren't also prefixed by Metadata_.

Usage

annotate(
  batch_id,
  plate_id,
  cell_id = NULL,
  external_metadata = NULL,
  format_broad_cmap = FALSE,
  output = NULL,
  perturbation_mode = "chemical",
  workspace_dir = "."
)

Arguments

batch_id	Batch ID.
plate_id	Plate ID.
cell_id	Optional cell ID. default: NULL.
external_metadata	Optional external metadata to join with, as a CSV file. default: NULL.
format_broad_cmap	Add columns for compatibility with Broad CMap naming conventions. default: FALSE.
output	Output file (.CSV) for annotated data. If NULL, writes to workspace_dir/backend/batch_id/plate_id/plate_id_augmented.csv. default: NULL.
perturbation_mode	Perturbation mode. Must be one of "chemical" or "genetic". default: "chemical".
workspace_dir	Root directory containing backend and metadata subdirectories. Can be relative or absolute. default: ".".

cytomining/cytotools documentation built on Nov. 19, 2020, 10:23 p.m.