gc_plot

Create GC histogram and delta-GC plot.

Provides a two-pane plot suitable for assessing the GC distribution of sequences within a genome bin. The first pane is a histogram of the percentage of non-overlapping windows (5 kbp by default; see -w) with a given percent GC. A typical genome will produce a unimodal distribution. The second pane plots each sequence in the genome bin as a function of its deviation from the average GC of the entire genome (x-axis) and sequence length (y-axis). The dashed red lines indicate the expected deviation from the mean GC as a function of length. This expected deviation is pre-calculated from a set of trusted reference genomes and the percentile plotted is provided as an argument to this command (dist_value). A good default value to use for this distribution parameter is 95.

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

Arguments

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

Create GC histogram and delta-GC plot.

positional arguments:
  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, --gc_window_size GC_WINDOW_SIZE
                        window size used to calculate GC histogram (default: 5000)
  -b, --gc_bin_width GC_BIN_WIDTH
                        width of GC bars in histogram (default: 0.01)
  -q, --quiet           suppress console output

Example: checkm gc_plot ./bins ./plots 95

Example

checkm gc_plot ./bins ./plots 95