CGR is a way of visualising strings into a scatterplot, with each recursive quadrant of the square represeting different substrings, see below [1].
E.g.
This is an example from a chromosome of Xestia xanthographa:
And the mitochondrion from the same species:
For now, plots are output to PNG for speed, however I may try and implement something interactive in JS.
As with other Rust projects, you have to complile yourself. Download rust, clone this repo, and then run:
cargo build --release
The executable will be at the location ./target/release/cgr.
cgr 0.1.0
Max Brown <[email protected]>
Make chaos game representations of a fasta file.
USAGE:
cgr [OPTIONS] --fasta <fasta>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-f, --fasta <fasta> The fasta file
-g, --grid <grid> Should the matrix be overlayed with a grid? [default: false] [possible values: true, false]
-o, --order <order> Order of the grid lattice. [default: 2]
-s, --save <save> Should the matrix coordinates be saved? Warning: these files can be very large, and take a
while to write. [default: false] [possible values: true, false][1] Goldman, Nick. "Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences." Nucleic Acids Research 21.10 (1993): 2487-2491.