Comments (2)
Okay, so let's try plotting a polarized -log10 pvalue—if KxKn is greater than 1, it is to the right/above the axis by an amount proportional to the -log10 pvalue.
scores = pd.read_table('ElementWiseScores - Sheet1.tsv', index_col=0)
for i,e in enumerate(scores.Type.unique()):
hits = scores.loc[scores.Type == e]
scatter(- np.sign(log(hits.KdKn)) * np.log10(hits.p_KdKn), -
np.sign(log(hits.KuKn))*np.log10(hits.p_KuKn), marker=['p', '*'][i], label=e)
lspine = ax.spines['left']
rspine = ax.spines['right']
rspine.set_alpha(0)
lspine.set_position(('data', 0))
ax.spines['bottom'].set_position(('data', 0))
ax.spines['top'].set_alpha(0)
legend(loc='center left')
for ix in scores.index:
text(-log10(scores.p_KdKn[ix])*sign(log(scores.KdKn[ix])), -log10(scores.p_KuKn[ix])*sign(log(scores.KuKn[ix])), ix)
Okay, so that figure is really busy, and actually dispels a trend I thought I saw that KdKn (x axis) was significantly more likely to be less than 1 (not obviously true), while KuKn was more likely to be above 1 (almost certainly true).
from mpra_selection.
From Hunter:
could you try randomly shuffling the expr change assigned to each mutation and see if the significant results go away, as a negative control?
and could you generate all the trees with up/down-reg indicated on each branch (either by color or numbers)? we could pick a couple for the main figs, and the rest could go in the supp.
from mpra_selection.
Related Issues (11)
- Decide what to do when there's not complete saturation of the mutagenesis HOT 1
- Merge Reconstructions doesn't work with snakemake on the cluster
- Think more closely about what to do with bases where we have data on deletions
- Make sure to process exonic enhancers differently HOT 2
- Deal with LINE elements HOT 3
- Deal with internal node if sequence same as parent
- Make changes to allow software to run more easily on different computers HOT 1
- BLAST can sometimes not return any hits in Rodents HOT 1
- Think about comparison with ancestral reconstruction MPRAs HOT 1
- Have some method to specify target ingroup 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 mpra_selection.