dist_plot

Create image with GC, CD, and TD distribution plots together.

Produces a single figure combining the plots produced by gc_plot, coding_plot, and tetra_plot.

This plot requires a file indicating the tetranucleotide signature of all sequences within the genome bins. This file can be created with the tetra command. 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>.ref_dist_plots.<image_type>.

Arguments

usage: checkm dist_plot [-h] [--image_type {eps,pdf,png,ps,svg}] [--dpi DPI]
                        [--font_size FONT_SIZE] [-x EXTENSION] [--width WIDTH] [--height HEIGHT]
                        [-a GC_WINDOW_SIZE] [-b TD_WINDOW_SIZE] [-c CD_WINDOW_SIZE]
                        [-1 GC_BIN_WIDTH] [-2 TD_BIN_WIDTH] [-3 CD_BIN_WIDTH] [-q]
                        results_dir bin_input output_dir tetra_profile dist_value [dist_value ...]

Create image with GC, CD, and TD distribution plots together.

positional arguments:
  results_dir           directory specified during analyze command
  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
  tetra_profile         tetranucleotide profiles for each sequence (see tetra command)
  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: 8)
  -a, --gc_window_size GC_WINDOW_SIZE
                        window size used to calculate GC histogram (default: 5000)
  -b, --td_window_size TD_WINDOW_SIZE
                        window size used to calculate TD histogram (default: 5000)
  -c, --cd_window_size CD_WINDOW_SIZE
                        window size used to calculate CD histogram (default: 10000)
  -1, --gc_bin_width GC_BIN_WIDTH
                        width of GC bars in histogram (default: 0.01)
  -2, --td_bin_width TD_BIN_WIDTH
                        width of TD bars in histogram (default: 0.01)
  -3, --cd_bin_width CD_BIN_WIDTH
                        width of CD bars in histogram (default: 0.01)
  -q, --quiet           suppress console output

Example: checkm dist_plot ./output ./bins ./plots tetra.tsv 95

Example

checkm tetra seqs.fna tetra.tsv
checkm dist_plot ./output ./bins ./plots tetra.tsv 95