Render

This module performs the extraction of useful metrics, and uses them to generate a series of summary plots, in PNG, HTML or PDF format.

Usage

The minimal command is cl render --input-path <PATH> --output-path <PATH>, where input-path is the path to the AVITI data folder and output-path is the directory where the plots will be placed.

Options

• --stats-json: Path to the cell2stats 'RunStats.json' file. Required only if different from <INPUT_PATH>/RunStats.json.
• --panel-json: Path to the cell2stats 'Panel.json' file. Required only if different from <INPUT_PATH>/Panel.json.
• --raw-parquet: Path to the cell2stats 'RawCellStats.parquet' file. Required only if different from <INPUT_PATH>/RawCellStats.parquet.
• --wells: Comma-separated list of wells to include in the analysis. By default, all wells will be used.
• --batches: Comma-separated list of batches to include in the analysis. By default, all batches will be used.
• --plot-list: Comma-separated list of plots to generate. Accepted values include 'All', 'BatchWell', 'Well', 'Count', 'Correlation', 'UMAP'. Default: All.
• --format: It can be one of 'html', 'png' or 'pdf'. Default is 'png'.