poonlab / plodex Goto Github PK
View Code? Open in Web Editor NEWInteractive visualization of SARS-CoV-2 variants
License: GNU Affero General Public License v3.0
Interactive visualization of SARS-CoV-2 variants
License: GNU Affero General Public License v3.0
Should these data be stored as a CSV instead?
> foo[foo$year==2019,]
region country year week mut.type mut.pos mut.diff count
5676 Asia China 2019 1 ~ 15 A 1
5677 Asia China 2019 1 ~ 20581 A 1
5678 Asia China 2019 1 ~ 20590 A 1
5679 Asia China 2019 1 ~ 21048 G 1
5680 Asia China 2019 1 ~ 21227 A 1
5681 Asia China 2019 1 ~ 21567 A 1
5682 Asia China 2019 1 ~ 22 C 1
5683 Asia China 2019 1 ~ 23 G 1
5684 Asia China 2019 1 ~ 24236 G 3
5685 Asia China 2019 1 ~ 30 G 1
5686 Asia China 2019 1 ~ 31 C 1
5687 Asia China 2019 1 ~ 35 A 1
5688 Asia China 2019 1 ~ 6907 C 1
5689 Asia China 2019 1 ~ 6927 A 1
5690 Asia China 2019 1 ~ 7912 C 1
5691 Asia China 2019 1 ~ 9445 T 1
5692 Asia China 2019 52 ~ 11675 A 1
5693 Asia China 2019 52 ~ 3689 G 1
5694 Asia China 2019 52 ~ 6879 A 1
5695 Asia China 2019 52 ~ 8299 G 1
5696 Asia China 2019 52 ~ 8898 A 1
It shouldn't be possible that genomes were sampled in January 2019.
Some genomes have an enormous number of differences from the references and are most likely problematic entries in the database.
I modified the parse_fasta.py
script to output a long listing of genome collection dates and numbers of genetic differences:
for qname, diffs, missing in encoder:
region, country, coldate = parse_header(qname, regions, typos)
args.outfile.write('{},{}\n'.format(coldate, len(diffs)))
sys.exit()
and wrote the output to data/clock.csv
.
Next, plotted the result in R:
clock <- read.csv('~/git/plodex/data/clock.csv')
clock$coldate <- as.Date(clock$coldate)
plot(clock$coldate, clock$count, cex=0.5)
Just realized that storing mutation counts provides no information on the number of genomes sampled from a given country at a given date, i.e., the denominator of these counts.
Recording the prevalence of mutations by calendar date, as well as by country, is too low level precision and would result in an enormous data file.
I am leaning towards RMarkdown to generate an HTML document "narrative".
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.