tetra_plot

Create tetranucleotide distance (TD) histogram and delta-TD plot.

Provides a plot analogous to the gc_plot suitable for assessing the tetranucleotide signatures of sequences within a genome bin. The Manhattan distance is used to determine the difference between each sequence’s tetranucleotide signature and the tetranucleotide signature of the entire genome bin.

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>.tetra_dist_plots.<image_type>.

Arguments

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

Create tetranucleotide distance (TD) histogram and delta-TD 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
  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: 3.5)
  -w, --td_window_size TD_WINDOW_SIZE
                        window size used to calculate TD histogram (default: 5000)
  -b, --td_bin_width TD_BIN_WIDTH
                        width of TD bars in histogram (default: 0.01)
  -q, --quiet           suppress console output

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

Example

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