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A python package for circDraw visualization and server command line interface

Project description

circDraw-py

PyPI version

This is a stand alone project which extends the power of circDraw service.

Dependency

Usage: Draw with circDraw

CircDraw provides python package to use when drawing circular RNA with the emphasis on backspliting sites visulization and epigenetic marker display. Import circDraw class via your favourite python3 interpreter or enbed it inside a script to use the drawing function.

from circDraw import circDraw

 # initiate a circDraw instance
cd = circDraw()

# set color of circ_on_chr (optional)
cd.set_palette(["#5CA0F2", "#FF881D", '#e30067', '#924900','#ab9c00','#ccd0d2', '#075800', '#5e0094',])

# set color of modifications (optional)
mod_palette = {'m6a': '#E98B2A',
               'm5c': '#E16B8C',
               'm1a': '#64363C',
               'pu': '#ffa12c',
               '2ome': '#1a6f00',
               'mre': '#6D2E5B',
               'rbp': "#2B5F75",
               'orf': '#516E41'}
cd.set_mod_palette(mod_palette)

# draw backsplicing site on chromosome region
cd.circ_on_chr('/path/to/file')

# draw modifications on circRNA
cd.mod_on_circ('/path/to/file')

Method

circ_on_chr

circDraw.circ_on_chr(file, title='circDraw', dpi=300, save='png', show=True, size=(10, 5))
  • File:

    • Only supported 'csv'

    • Start End Type Name Color (Optional)
    • Start < End

    • Type: circ, exon, intron, gene

    • Color: RGB, RGBA, hex, or supported color names.

  • Title: The title of the plot

  • Save: file format you wish to save as, PNG, PDF, JPEG, etc.

  • Show: Bool, wheather to show the plot after rendering.

  • Size: (Length, Width) the size of the plot.

mod_on_circ

circDraw.mod_on_circ(self, file, dpi=100, save='png', show=True, size=(7, 7), sep_mod=False)
  • File:

    • Only supported 'csv'

    • Start End Type Name Color (Optional)
    • Start < End

    • Type: circ, exon, intron, and modifications type

      • Modifications type: m6A, m1A, m5C, pU, 2OMe, MRE, RBP, ORF
    • Color: RGB, RGBA, hex, or supported color names.

  • Save: file format you wish to save as, PNG, PDF, JPEG, etc.

  • Show: Bool, wheather to show the plot after rendering.

  • Size: (Length, Width) the size of the plot.

  • sep_mod: Bool, prevent the modifications from overlapping if set True.

set_palette

circDraw.set_palette(palette)

A list of colors, the length of the list must bigger than 5.

set_mod_palette

circDraw.set_mod_palette(palette)

A dictionary of colors match with the modification. You can change any one of the modification colors.

More information

This a part of circDraw project. Please visit our Contact page if you have any questions.

Copyright: Qu Lab, School of Life Science, Sun Yat-sen University, Guangzhou, CHINA.

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