Circos-Py

B-Cell Clones as Circos Plots

This script was made to illustrate the expansion of B-cell clones over multiple timepoints by converting a spreadsheet input to a Circos plot. In this specific case, the orange and blue colors depict specific B-cell phenotypes.

With the circos-py repository installed and setup, the above plot can be generated by navigating to the circos-py directory at the command line and running the make_circos_plots.py script with the example input data as shown below.

cd ~/circos-py
python make_circos_plots.py example_input_data.csv

Install

Quick-Guide

Just a quick gerneral guide for Mac users: if you do not actively use Python, Perl, or Circos already I would recommend installing Anaconda3, then installing Perl via conda:

conda install -c anaconda perl

Then install Circos, unzip, and symlink to usr/local/bin:

cd ~/Desktop
wget http://circos.ca/distribution/circos-0.69-6.tgz
tar xvfz circos-0.69-6.tgz
ln -s ~/Desktop/circos-0.69-6/bin/circos /usr/local/bin/circos

You should now be able to run circos from the command line. Check this by running the following from the terminal:

$ circos -v

And you should see something similar to:

circos | v 0.69-6 | 31 July 2017 | Perl 5.022000

Now it's time to check what Perl modules are needed to run Circos: circos -module

A list of modules should sputter forth. Use the below snippet to install all Circos Perl modules with CPAN:

cpan Carp Clone Config::General Cwd Data::Dumper Digest::MD5 File::Basename File::Spec::Functions File::Temp FindBin Font::TTF::Font GD GF::Polyline Getopt::Long IO::File List::MoreUtils List::Util Math::Bezier Math::BigFloat Math::Round Math::VecStat Memoize POSIX Params::Validate Pod::Usage Readonly Regexp::Common SVG Set::IntSpan Statistics::Basic Storable Sys::Hostname Text::Balanced Text::Format Time::HiRes

Last thing is to clone this repository:

git clone [email protected]:greenkidneybean/circos-py.git

Circos

Unfortunately Circos takes a bit of effort to get up and running. I swear at one point I was albe to install via Homebrew, but if that's kaput then head straight to the source: Circos

Circos-Py

Setup

Add Circos Binary to Your Shell Path

Changes in the Circos Defaults

I've included my Circos configuration files which use fonts that are not included in the Circos Plot package. Circos supports true type (.ttf) and open type (.otf) fonts, which can be added to the Circos package (fonts/modern/). To use an added font you must add a key term to the Circos fonts file (etc/fonts.conf) and the path to the font. For example:

arial_bold = fonts/modern/Arial Bold.ttf

I'm also delimiting all my data files (karyotype and links) with tabs instead of spaces (the default). This can be changed in housekeeping.conf file (etc/housekeeping.conf).

file_delim = \t

Input File Requirements

• Input file must be an Excel workbook (.xlsx)
  • Each sample must have its own sheet
  • The sheet name will be used as a label for all data generated from that sheet
• Each sheet requires the following 4 columns
  • timepoint - identifies the timepoint from which the sequence was derived
  • clone - used to assign the sequence to a clone group
  • seq_id - unique identifier for the sequence
  • spec - phenotypic or subpopulation information

Output Circos Plots

ToDo:

• Add two more sample to example data
• requirements?
• create circos module with all functions
• Lock package dependencies
• Web GUI