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"author": "Anthony Aylward, Joshua Chiou, Mei-Lin Okino",
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"description": "# luciferase\nTool for plotting luciferase reporter data. Thanks due to Joshua Chiou and Mei-lin Okino for inspiration and contributions.\n\n## Installation\n```sh\npip3 install luciferase\n```\nor\n```sh\npip3 install --user luciferase\n```\n\n## Command-line interface for barplots\n\n### Barplots of enhancer activity\n\nA script called `luciferase-barplot` for creating bar plots from JSON-formatted\ndata is included. After installing `luciferase`, you can use it like this:\n```sh\nluciferase-barplot --title \"plot title\" example.json example.pdf \n```\n\nSee also the help message:\n```sh\nluciferase-barplot -h\n```\n\nExamples of luciferase reporter data in JSON format:\n```json\n{\n \"Non-risk, Fwd\": [8.354, 12.725, 8.506],\n \"Risk, Fwd\": [5.078, 5.038, 5.661],\n \"Non-risk, Rev\": [9.564, 9.692, 12.622],\n \"Risk, Rev\": [10.777, 11.389, 10.598],\n \"Empty\": [1.042, 0.92, 1.042]\n}\n```\n```json\n{\n \"Alt, MIN6\": [5.47, 7.17, 6.15],\n \"Ref, MIN6\": [3.16, 3.04, 4.34],\n \"Empty, MIN6\": [1.07, 0.83, 0.76],\n \"Alt, ALPHA-TC6\": [2.50, 3.47, 3.33],\n \"Ref, ALPHA-TC6\": [2.01, 1.96, 2.31],\n \"Empty, ALPHA-TC6\": [1.042, 0.92, 1.042]\n}\n```\n\nThe input JSON should contain either five, six, or twelve entries. If it\ncontains five entries, the bars of the resulting plot will have a 2-2-1 style.\nIf it contains six entries, the bars will have a 2-1-2-1 style. If twelve,\nthe syle will be as with six entries but doubled.\n\nSignificance indicators will be written above the bars: `***` if p<0.001,\n`**` if p<0.01, `*` if p<0.05, `ns` otherwise.\n\nHere is an example of a plot in the 2-1-2-1 style:\n\n\n\n\n### Barplots of allelic ratio\n\nA second script called `luciferase-ratioplot` takes the same input data and\nproduces a comparative plot of allelic ratios:\n\n```sh\nluciferase-ratioplot --title \"plot title\" example.json example.pdf\n```\n\nFor this script, the number of entries in the input JSON should be a multiple\nof 3. The resulting plot shows the estimated allelic ratio of enhancer activity\nwith confidence intervals (95% by default). Here is an example input dataset\nand plot:\n\n```json\n{\n \"Alt, dex\": [44.6, 37.6, 37.7],\n \"Ref, dex\": [149.4, 99.7, 124.5],\n \"Empty, dex\": [1.1, 1.0, 0.9],\n \"Alt, untreated\": [19.7, 16.2, 18.3],\n \"Ref, untreated\": [33.2, 30.3, 33.3],\n \"Empty, untreated\": [1.0, 1.0, 1.0]\n}\n```\n\n\n## Meta-analysis\n\nIt may be that we have performed two or more experiments\n(from separate minipreps) and wish to meta-analyze the results. As an example,\nlet's consider the results of two identical experiments on a regulatory\nvariant at the _SIX3_ locus: [SIX3-MP0](https://github.com/anthony-aylward/luciferase/raw/master/example/six3-mp0.json) and [SIX3-MP1](https://github.com/anthony-aylward/luciferase/raw/master/example/six3-mp1.json). First we'll plot both datasets separately:\n```sh\nluciferase-barplot six3-mp0.json six3-mp0.png --light-colors '#DECBE4' '#FED9A6' '#FBB4AE' --dark-colors '#984EA3' '#FF7F00' '#E41A1C' --title 'SIX3-MP0'\nluciferase-barplot six3-mp1.json six3-mp1.png --light-colors '#DECBE4' '#FED9A6' '#FBB4AE' --dark-colors '#984EA3' '#FF7F00' '#E41A1C' --title 'SIX3-MP1'\n```\n\n![](\"https://github.com/anthony-aylward/luciferase/raw/master/example/six3-mp0.png\")
![](\"https://github.com/anthony-aylward/luciferase/raw/master/example/six3-mp1.png\")
\n\nWe can see that the results are fairly consistent in character, but checking\nthe y-axis tells us that they are on different scales. Intuitively, we might\nconclude from these results that there are allelic effects under all three\nconditions. Ideally though, we would like to use all of the data at once for\none plot to get the most accurate conclusions about allelic effects.\n\nWe might simply combine the data into one dataset, (as [here](https://github.com/anthony-aylward/luciferase/raw/master/example/six3-meta-nobatch.json)) and plot it:\n```sh\nluciferase-barplot six3-meta-nobatch.json six3-meta-nobatch.png --light-colors '#DECBE4' '#FED9A6' '#FBB4AE' --dark-colors '#984EA3' '#FF7F00' '#E41A1C'\n```\n\n\n\nThe bar heights look reasonable, and the allelic effects appear clear from\nlooking at them, but all of the hypothesis tests returned non-significant\nresults. What gives?\n\nThe answer is that combining data from experiments with different scales\nbreaks the assumptions of the significance test (a t-test). To meta-analyze\nthese data in a useful way, we first need to re-normalize the two experiments\nto put both of them on the same scale. `luciferase-barplot` will re-normalize\nthe data automatically if the dataset includes an additional entry (\"Batch\")\nindicating the batch of each data point, as in this example:\n[SIX3-META](https://github.com/anthony-aylward/luciferase/raw/master/example/six3-meta.json).\n```json\n{\n \"Alt, untreated\": [19.7, 16.2, 18.3, 6.5, 8.0, 4.4],\n \"Ref, untreated\": [33.2, 30.3, 33.3, 8.4, 13.6, 17.1],\n \"Empty, untreated\": [1.0, 1.0, 1.0, 1.1, 1.0, 0.9],\n \"Alt, hi_cyt_noTNFA\": [11.0, 8.8, 10.1, 3.2, 3.7, 3.3],\n \"Ref, hi_cyt_noTNFA\": [17.1, 16.7, 18.8, 7.6, 6.7, 5.5],\n \"Empty, hi_cyt_noTNFA\": [1.1, 0.9, 1.0, 1.1, 0.9, 1.0],\n \"Alt, hi_cyt\": [10.8, 10.9, 9.1, 3.1, 2.7, 4.0],\n \"Ref, hi_cyt\": [17.8, 16.1, 18.0, 7.7, 7.0, 7.1],\n \"Empty, hi_cyt\": [1.0, 1.0, 1.0, 1.0, 1.0, 1.1],\n \"Batch\": [0, 0, 0, 1, 1, 1]\n}\n```\n\nHere is what the results look like when they're re-normalized to correct for\nbatch\n```sh\nluciferase-barplot six3-meta.json six3-meta.png --light-colors '#DECBE4' '#FED9A6' '#FBB4AE' --dark-colors '#984EA3' '#FF7F00' '#E41A1C' --title 'SIX3-META'\n```\n\n\n\n\n",
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