Comments (4)
@trvrb I've implemented this as a post-augur export
step. (In augur v6, augur export
will be able to do this, but I think we want SFS to run on augur v5.)
Steps needed for the snakefile:
(1) rule export_aggregated
should save the tree JSON into "./results", (the meta JSON should be saved in "./auspice" as it is currently.
(2):
python scripts/annotate_hidden_nodes.py \
--input results/seattle_flu_seasonal_h3n2_genome_2y_tree.json \
--output auspice/seattle_flu_seasonal_h3n2_genome_2y_tree.json
This script has the side effect of labeling internal nodes with the cluster (previously only terminal nodes).
from augur-build.
Branch exploded Now modified to remove the trailing branch & maximize what's shown in auspice -- see cef2d75 for more info.
from augur-build.
@trvrb if you modify https://github.com/seattleflu/augur-build/blob/exploded/scripts/annotate_hidden_nodes.py#L53 to be, e.g.
"attr": {
"num_date": node["attr"]["num_date"] - 1/12,
"div": node["attr"]["div"] - 0.0002
},
Then you'll have little stubs which you can click on to zoom into each cluster, like so:
from augur-build.
Thanks @jameshadfield! This is great.
from augur-build.
Related Issues (11)
- Swap out reference for a more recent virus HOT 3
- Nucleotide length in reference .gb file HOT 3
- Create reproducible coloring for census tracts
- Make filter-to-region optional in extract_cluster_fastas.py HOT 1
- Compare genetic distance to geographic distance
- Calculate genetic distance to closest sample HOT 1
- Filter cluster output HOT 5
- Clean up incoming ID3C data HOT 11
- Genome reference
- Missing header information in genome reference HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from augur-build.