Drawing (CLI)

This module allows you to draw plots using the command line.

Note

Draw is written primarily for Python. See the page Plots / Get started to use draw with Python. It contains more plots and more options.

Examples

# Plots mutation_fraction, mutation_fraction_identity, and base_coverage
dreem draw --inpt my_test_sample.json

# Plots only the mutation_fraction plot
dreem draw --inpt my_test_sample.json --mutation_fraction

# Plots only the specified regions for each reference
dreem draw --inpt my_test_sample.json -c reference_1 17 69 -c reference_2 18 21

# Get a structured output
dreem draw --inpt my_test_sample.json --flat 0

# Give name to the sections in the output names
dreem draw --inpt my_test_sample.json --flat 0 --library library.csv

API Reference

CLI cmds

dreem draw

dreem draw [OPTIONS]

Options

--inpt <inpt>: Path to a dreem output format file. Can be specified multiple times.

--out-dir <out_dir>: Where to output all finished files

--flat, --no-flat: Flatten the output folder structure. This names your files [reference]__[section]__[plot_name].html

-c, --coords <coords>: Reference name, 5’ end, and 3’ end of a section; coordinates are 1-indexed and include both ends

--section <section>: Section to draw. Can be specified multiple times.

-mf, --mutation_fraction: Plot mutation_fraction plot. See Plots/gallery.

-mfi, --mutation_fraction_identity: Plot mutation_fraction_identity plot. See Plots/gallery.

-bc, --base_coverage: Plot base_coverage plot. See Plots/gallery.

-mib, --mutations_in_barcodes: Plot mutations_in_barcodes plot. See Plots/gallery.

-mprps, --mutation_per_read_per_reference: Plot mutation_per_read_per_reference plot. See Plots/gallery.

Python args

dreem.draw.run(inpt: tuple[str] = (), *, flat: list = True, out_dir: str = './output', coords: tuple = (), section: str = ('full',), mutation_fraction: bool = True, mutation_fraction_identity: bool = True, base_coverage: bool = True, mutations_in_barcodes: bool = False, mutation_per_read_per_reference: bool = True)

Run the draw command.

Parameters

inpt (tuple) – Path to a dreem output format file. Can be specified multiple times. [positional or keyword, default: ()]
flat (list) – Flatten the output folder structure. This names your files [reference]__[section]__[plot_name].html [keyword-only, default: True]
out_dir (str) – Where to output all finished files [keyword-only, default: ‘./output’]
coords (tuple) – Reference name, 5’ end, and 3’ end of a section; coordinates are 1-indexed and include both ends [keyword-only, default: ()]
section (str) – Section to draw. Can be specified multiple times. [keyword-only, default: (‘full’,)]
mutation_fraction (bool) – Plot mutation_fraction plot. See Plots/gallery. [keyword-only, default: True]
mutation_fraction_identity (bool) – Plot mutation_fraction_identity plot. See Plots/gallery. [keyword-only, default: True]
base_coverage (bool) – Plot base_coverage plot. See Plots/gallery. [keyword-only, default: True]
mutations_in_barcodes (bool) – Plot mutations_in_barcodes plot. See Plots/gallery. [keyword-only, default: False]
mutation_per_read_per_reference (bool) – Plot mutation_per_read_per_reference plot. See Plots/gallery. [keyword-only, default: True]

I/O files

Input

sample_1.json
sample_2.json
...

Output

sample_1/
  |- construct_1/
      |- 3_27/  # start and end position of the section, 1-based
          |- mutation_fraction.html
          |- mutation_fraction_identity.html
          |- base_coverage.html
       ...
   ...
sample_2/
   ...

Note

Use the --flat option to output the files in a flat structure:

sample_1/
  |- construct_1__3_27__mutation_fraction.html
  |- construct_1__3_27__mutation_fraction_identity.html
  |- construct_1__3_27__base_coverage.html
    ...
sample_2/
    ...

Edge cases handling

To avoid handling too many arguments in the commandline, only the most simple plots are supported. If you want to do more complex plots, you can use the Python API.

Contributors: Yves Martin des Taillades