chromocharts

Visualisations for chromosome analysis

Build Setup

# install dependencies
yarn install

# serve with hot reload at localhost:8080
yarn run dev

# build for production with minification
yarn run build

# build for production and view the bundle analyzer report
yarn run build --report

# run all tests
yarn run test

chromocharts

To use the chromosome component, use the example in ChromochartsOverview.vue.

cytoBandParser

To generate the chromosome data, use the python3 script: utils/cytobandParser.py This file parses the UCSC cytoband.txt file per chromosome and converts it to chromocharts format Example input file called chr.txt:

chrY	0	2500000	p11.32	gneg
chrY	2500000	3000000	p11.31	gpos50
chrY	3000000	11600000	p11.2	gneg
chrY	11600000	12500000	p11.1	acen
chrY	12500000	13400000	q11.1	acen
chrY	13400000	15100000	q11.21	gneg
chrY	15100000	19800000	q11.221	gpos50
chrY	19800000	22100000	q11.222	gneg
chrY	22100000	26200000	q11.223	gpos50
chrY	26200000	28800000	q11.23	gneg
chrY	28800000	59373566	q12	gvar

Output:

[[0, 2500000, "p11.32"], [2500000, 3000000, "p11.31"], [3000000, 11600000, "p11.2"], [11600000, 12500000, "p11.1"], [12500000, 13400000, "q11.1"], [13400000, 15100000, "q11.21"], [15100000, 19800000, "q11.221"], [19800000, 22100000, "q11.222"], [22100000, 26200000, "q11.223"], [26200000, 28800000, "q11.23"], [28800000, 59373566, "q12"]]