create_stat_heatmap - CLI interface

Create a site-statistic heatmap image.

create_stat_heatmap [-h] [--config_file CONFIG_FILE] [--log_filename LOG_FILENAME]
                    [--log_console] [-r REPORT_FILENAME] [-b BASE_LAYER] [-t TITLE]
                    [--cmap CMAP] [--vmin VMIN] [--vmax VMAX] [--mask_matrix MASK_MATRIX]
                    plot_filename matrix_filename {pearson_correlation,pearson_correlation}
                    min_x min_y max_x max_y resolution

create_stat_heatmap positional arguments

  • plot_filename - A file path to write the generated plot image. (default: None)

  • matrix_filename - The file path of the site-statistic matrix (of type ['covariance_stats', 'site_matrix_stats', 'site_tree_stats', 'site_tree_distance_matrix_stats', 'site_pam_dist_mtx_stats']) containing a statistic to map. (default: None)

  • statistic - The name of the statistic (must match column header) in the matrix. For each site-statistic matrix, its statistics columns are: (default: None)

  • min_x - The minimum x value of the plot map range. (default: None)

  • min_y - The minimum y value of the plot map range. (default: None)

  • max_x - The maximum x value of the plot map range. (default: None)

  • max_y - The maximum y value of the plot map range. (default: None)

  • resolution - The resolution of each cell of the plot map. (default: None)

create_stat_heatmap optional arguments

  • -h, --help - show this help message and exit

  • --config_file CONFIG_FILE - Path to configuration file. (default: None)

  • --log_filename LOG_FILENAME, -l LOG_FILENAME - A file location to write logging data. (default: None)

  • --log_console - If provided, write logging statements to the console.

  • -r REPORT_FILENAME, --report_filename REPORT_FILENAME - File location to write the summary report. (default: None)

  • -b BASE_LAYER, --base_layer BASE_LAYER - An optional base layer image for the plot. Must have same extent. (default: None)

  • -t TITLE, --title TITLE - A title to add to the plot image. (default: None)

  • --cmap CMAP - A color map to use for the image. (default: Reds)

  • --vmin VMIN - The minimum value for color scaling. (default: None)

  • --vmax VMAX - The maximum value for color scaling (use -1 to use maximum from data). (default: None)

  • --mask_matrix MASK_MATRIX - File path to a binary matrix to use as a mask. (default: None)