Comments (3)
This is possible from coverage histogram data, i.e, the output of panacus hist ...
, but requires you to manually merge the chromosome data together. This is simple, because they're just tables, and here is one way to do that with python/pandas:
import pandas as pd
FILES=['/your/list/of/chromosomes/chr1.hist.txt', '/your/list/of/chromosomes/chr2.hist.txt', ]
df = None
for f in FILES:
_df = pd.read_csv(f, sep='\t', header=[1], index_col=[0])
if df is None:
df = _df
else:
df += _df
with open('/your/output/file.hist.txt', 'w') as out:
df.reset_index().to_csv(out, sep='\t', index=False)
Then pass the output file to panacus, i.e., panacus growth /your/output/file.hist.txt
and you're good to go.
from panacus.
After panacus hist
and panacus growth
, the final visualization will show #nodes
instead of bps
. I use -c bp
for hist
from panacus.
from panacus.
Related Issues (20)
- What is the meaning of common and consensus? HOT 4
- Option to output plots in separate PNG files HOT 11
- Could you please make an new release? HOT 3
- command is not supported for more than 65534 HOT 6
- How to Visualize the results of the minigraph-cactus? HOT 21
- Request software updates HOT 6
- Feature request: Alternative plot with #nodes/#edges vs AC
- A problem while running panacus-visualize HOT 1
- Update Readme to reflect installation of python dependencies in the installation section. HOT 1
- compiler error in rustc-serialize HOT 3
- AttributeError: 'DataFrame' object has no attribute 'cumulative' HOT 13
- Haplotype labels in TSV, visualisations ? HOT 8
- panacus-visualize.py is overwhelmed by 1000 haplotypes HOT 10
- how is panacus treating Ns HOT 4
- What does the output content represent HOT 7
- could you give us an example of cactus? HOT 7
- Installation instructions HOT 2
- path coordinates HOT 8
- After `panacus hist` and `panacus growth`, the final visualization will show `#nodes` instead of `bps`. I use `-c bp` for hist 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 panacus.