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19. Plot Sample BGC ome

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Rauf Salamzade edited this page Apr 16, 2023 · 3 revisions

visualize_BGC-Ome.py

visualize_BGC-Ome.py is a standalone script that takes a single sample's BGC predictions results (as a directory) from antiSMASH, GECCO, or DeepBGC and uses the gggenes library in R to visualizae gene schematics of BGCs. Coloring corresponds to the BGC-likeness of genes. For antiSMASH this is a binary trait, either the gene contains a key 'rule'/'detection' domain, or not. For DeepBGC and GECCO this is based on the gene score or the maximum score of domains within genes, respectively.

Usage:

usage: visualize_BGC-Ome.py [-h] -b BGC_RESULTS_DIR [-p BGC_PREDICTION_SOFTWARE] [-o OUTPUT_PDF] [-t TMP_DIR] [-l LENGTH] [-w WIDTH]

        Program: visualize_BGC-Ome.py
        Author: Rauf Salamzade
        Affiliation: Kalan Lab, UW Madison, Department of Medical Microbiology and Immunology
        *******************************************************************************************************************
        Visualize the BGC-ome for a sample.

        Visualization is performed using the gggenes library in R. 

        Coloring basis:

        - For antiSMASH predictions: Discrete. "rule-based" key domain for detection containing genes are gold, rest are grey.  
        - For DeepBGC predictions: Continuous. score by model for BGC-likeness. 
        - For GECCO predictions: Continuous. score by model for BGC-likeness.


optional arguments:
  -h, --help            show this help message and exit
  -b BGC_RESULTS_DIR, --bgc_results_dir BGC_RESULTS_DIR
                        Sample-specific results directory from antiSMASH, DeepBGC, or GECCO.
  -p BGC_PREDICTION_SOFTWARE, --bgc_prediction_software BGC_PREDICTION_SOFTWARE
                        Software used to predict BGCs (Options: antiSMASH, DeepBGC, GECCO).
                        Default is antiSMASH.
  -o OUTPUT_PDF, --output_pdf OUTPUT_PDF
                        Path to output PDF file [Default is ./Sample_BGC-ome.pdf].
  -t TMP_DIR, --tmp_dir TMP_DIR
                        Path to temporary dir. [Default is ./tmp_dir_$INDIR_BASE_NAME].
  -l LENGTH, --length LENGTH
                        Specify the height/length of the heatmap plot. [Default is 7].
  -w WIDTH, --width WIDTH
                        Specify the width of the heatmap plot. [Default is 10].
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