coding_plot

Create coding density (CD) histogram and delta-CD plot.

Provides a plot analogous to the gc_plot suitable for assessing the coding density of sequences within a genome bin.

This command requires the output folder of the analyze, lineage_wf, or taxonomy_wf command (results_dir).

A plot is written for each bin to <output_dir>/<bin id>.coding_density_plots.<image_type>.

Arguments

usage: checkm coding_plot [-h] [--image_type {eps,pdf,png,ps,svg}] [--dpi DPI]
                          [--font_size FONT_SIZE] [-x EXTENSION] [--width WIDTH] [--height HEIGHT]
                          [-w CD_WINDOW_SIZE] [-b CD_BIN_WIDTH] [-q]
                          results_dir bin_input output_dir dist_value [dist_value ...]

Create coding density (CD) histogram and delta-CD plot.

positional arguments:
  results_dir           output directory of the analyze, lineage_wf or taxonomy_wf command (for marker_plot, qa must also have been run)
  bin_input             directory containing bins (fasta format) or path to file describing genomes/genes - tab separated in 2 or 3 columns [genome ID, genome fna, genome translation file (pep)]
  output_dir            directory to hold plots
  dist_value            reference distribution(s) to plot; integer between 0 and 100

options:
  -h, --help            show this help message and exit
  --image_type {eps,pdf,png,ps,svg}
                        desired image type (default: png)
  --dpi DPI             desired DPI of output image (default: 600)
  --font_size FONT_SIZE
                        Desired font size (default: 8)
  -x, --extension EXTENSION
                        extension of bins (other files in directory are ignored) (default: fna)
  --width WIDTH         width of output image (default: 6.5)
  --height HEIGHT       height of output image (default: 3.5)
  -w, --cd_window_size CD_WINDOW_SIZE
                        window size used to calculate CD histogram (default: 10000)
  -b, --cd_bin_width CD_BIN_WIDTH
                        width of CD bars in histogram (default: 0.01)
  -q, --quiet           suppress console output

Example: checkm coding_plot ./output ./bins ./plots 95

Example

checkm coding_plot ./output ./bins ./plots 95