marker_plot

Plot position of marker genes on sequences.

Plots the position of marker genes on sequences within a genome bin. This provides information regarding the extent to which marker genes are collocated. The number of marker genes within each fixed-size window along a sequence is indicated with different colours. Sequences without any marker genes are not shown.

This command requires the output folder of the analyze, lineage_wf, or taxonomy_wf command (results_dir), and the qa command must also have been run on this folder (the workflows run qa).

A plot is written for each bin with marker genes to <output_dir>/<bin id>.marker_pos_plot.<image_type>.

Arguments

usage: checkm marker_plot [-h] [--image_type {eps,pdf,png,ps,svg}] [--dpi DPI]
                          [--font_size FONT_SIZE] [-x EXTENSION] [--width WIDTH] [--height HEIGHT]
                          [--fig_padding FIG_PADDING] [-q]
                          results_dir bin_input output_dir

Plot position of marker genes on sequences.

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

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: 6.5)
  --fig_padding FIG_PADDING
                        white space to place around figure (in inches) (default: 0.2)
  -q, --quiet           suppress console output

Example: checkm marker_plot ./output ./bins ./plots

Example

checkm marker_plot ./output ./bins ./plots