domainator plot_contigs
Draw contigs and their annotations as an interactive HTML page.
Create graphical representations of the contigs and their annotations
It works best for relatively small datasets, of a few megabases or a few hundred contigs.
Give at least one of these outputs: --html_out. - as an input or output means standard input or output, where the option says it is allowed.
| Option | Value | Default | Description |
|---|---|---|---|
-v, --verbose |
show debug output, and a traceback for errors. | ||
-q, --quiet |
show errors only: no progress messages or warnings. | ||
-i, --input |
FILE ... | required | names of input genbank files. Use - to read standard input. |
-o, --html_out |
FILE | required | Write the plot to this html file. Use - for standard output. |
--height |
INTEGER | 2400 | height of the contig plot, in pixels |
--width |
INTEGER | 1200 | width of the contig plot, in pixels |
--types |
STRING ... | Feature types to include in the plot. Default is 'CDS exon repeat_region ncRNA rRNA tRNA Domainator Domain_Search'. | |
--feature_height |
INTEGER | 50 | height of the feature arrows, in pixels. |
--feature_font_size |
INTEGER | 26 | font size of the feature labels, in pixels. |
--metadata |
FILE ... | tab separated files of additional contig metadata. | |
--color_by |
STRING | Color the contig lines in the plot based on this column of the metadata table. | |
--color_table |
FILE | tab separated file with two columns and no header: a --color_by value and a hex color, for example: CCDB cc0000. Without it, colors are assigned automatically. | |
--palette_offset |
INTEGER | 0 | Skip this many colors at the start of the palette before assigning colors to --color_by values. For example, if a plot colored by one column used the first 5 colors, --palette_offset 5 colors another column without reusing them. Ignored with --color_table. |
Every command also takes --config FILE (options from a JSON or YAML file, keyed by option name) and --print_config.