annotate: Add plate and well metadata.

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

Add plate and well metadata.

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 Sept. 18, 2024, 11:58 p.m.