Helper functions for luciferase data
Project description
luciferase
Tool for plotting luciferase reporter data. Thanks due to Joshua Chiou and Mei-lin Okino for inspiration and contributions.
Installation
pip3 install luciferase
or
pip3 install --user luciferase
Command-line interface for barplots
Barplots of enhancer activity
A script called luciferase-barplot
for creating bar plots from JSON-formatted
data is included. After installing luciferase
, you can use it like this:
luciferase-barplot --title "plot title" example.json example.pdf
See also the help message:
luciferase-barplot -h
Examples of luciferase reporter data in JSON format:
{
"Non-risk, Fwd": [8.354, 12.725, 8.506],
"Risk, Fwd": [5.078, 5.038, 5.661],
"Non-risk, Rev": [9.564, 9.692, 12.622],
"Risk, Rev": [10.777, 11.389, 10.598],
"Empty": [1.042, 0.92, 1.042]
}
{
"Alt, MIN6": [5.47, 7.17, 6.15],
"Ref, MIN6": [3.16, 3.04, 4.34],
"Empty, MIN6": [1.07, 0.83, 0.76],
"Alt, ALPHA-TC6": [2.50, 3.47, 3.33],
"Ref, ALPHA-TC6": [2.01, 1.96, 2.31],
"Empty, ALPHA-TC6": [1.042, 0.92, 1.042]
}
The input JSON should contain either five, six, or twelve entries. If it contains five entries, the bars of the resulting plot will have a 2-2-1 style. If it contains six entries, the bars will have a 2-1-2-1 style. If twelve, the syle will be as with six entries but doubled.
Significance indicators will be written above the bars: ***
if p<0.001,
**
if p<0.01, *
if p<0.05, ns
otherwise.
Here is an example of a plot in the 2-1-2-1 style:
Barplots of allelic ratio
A second script called luciferase-ratioplot
takes the same input data and
produces a comparative plot of allelic ratios:
luciferase-ratioplot --title "plot title" example.json example.pdf
For this script, the number of entries in the input JSON should be a multiple of 3. The resulting plot shows the estimated allelic ratio of enhancer activity with confidence intervals (95% by default). Here is an example input dataset and plot:
{
"Alt, dex": [44.6, 37.6, 37.7],
"Ref, dex": [149.4, 99.7, 124.5],
"Empty, dex": [1.1, 1.0, 0.9],
"Alt, untreated": [19.7, 16.2, 18.3],
"Ref, untreated": [33.2, 30.3, 33.3],
"Empty, untreated": [1.0, 1.0, 1.0]
}
Meta-analysis of luciferase reporter data
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