Wednesday 21 November 2018

Plotting chromosomes using Python pysvg

To draw an svg image of chromosomes, here is a little example I made using pysvg (below).

I found some nice examples for using pysvg here.
Here is another old example (seems to use an old version of pysvg, that doesn't work now) by Noel O'Blog.

It can be run using python2 (not python3):
% python /nfs/users/nfs_a/alc/Documents/git/Python/ emu_chrs.svg
% convert emu_chrs.svg emu_chrs.png

The output looks like (as png):

You can edit it manually in the SVG editor Inkscape (Note to self: do 'ssh -Y pcs5' and then 'inkscape emu_chrs.svg').

The code is:

import sys
import os
import pysvg.structure
import pysvg.text

# Note: this is to make a svg plot with the E. multilocularis chromosomes,
# plotted one under the other, scaled according to their lengths, and
# with a different colour for each chromosome, and a label for each
# chromosome.
# Note 2: this script must be run with python2 (not python3).


def define_input_data():
    # define the input data, as a list of E. multilocularis chromosomes, and
    # a dictionary with lengths of E. multilocularis chromosomes, and a dictionary
    # with the colours to plot E. multilocularis chromosomes:

    chrlist = ["chr1", "chr2", "chr3"]
    chrlengths = { "chr1": 2000000, "chr2": 5000000, "chr3": 4500000}
    chrcols = { "chr1": "rgb(255,0,153)", "chr2": "blue", "chr3": "purple"}
    # Note: there is a list of RGB values for colours here:

    return(chrlist, chrlengths, chrcols)


# make the plot of the input data:

def plot_input_data(chrlist, chrlengths, chrcols, output_svg_file):

    # initialise our svg picture  
    svg_document = pysvg.structure.Svg()
    shape_builder =

    # plot each chromosome, one under the other:
    chrcnt = 0
    yscale = 100
    xscale = 0.00004
    for mychr in chrlist:
        # find its length:

        assert(mychr in chrlist)
        mychrlen = chrlengths[mychr]
        # find the colour to plot it:
        assert(mychr in chrcols)
        mychrcol = chrcols[mychr]
        # add a rectangle to our svg picture for this chromosome:
        # createRect takes x, y, width, height
        myrectwidth = "%dpx" % (mychrlen*xscale + 20)
        svg_document.addElement(shape_builder.createRect(0, chrcnt*yscale, myrectwidth, "50px", strokewidth = 1, stroke = "black", fill = mychrcol))
        # add some text to our svg picture for this chromosome:
        svg_document.addElement(pysvg.text.Text(mychr, x = mychrlen*xscale + 30, y = chrcnt*yscale + 30))
        # add one to the chromosome count:
        chrcnt += 1

    # save the svg picture to an output file



def main():
    # check the command-line arguments:
    if len(sys.argv) != 2:
        print("Usage: %s output_svg_file" % sys.argv[0])
    output_svg_file = sys.argv[1]

    # define the input data: (note: you could read this in from an input file)
    (chrlist, chrlengths, chrcols) = define_input_data()

    # make the plot of the input data:
    plot_input_data(chrlist, chrlengths, chrcols, output_svg_file)


if __name__=="__main__":


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