luciferase 1.3.14

Helper functions for luciferase data

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.