diff --git a/algo/core/windows.cpp b/algo/core/windows.cpp index d1c6730653756639215f006dc4ff28a3b2ca9896..6fb0bc8ad9560749f128f70e567839e6123bb49c 100644 --- a/algo/core/windows.cpp +++ b/algo/core/windows.cpp @@ -266,7 +266,7 @@ json WindowsStorage::computeDiversity(map nb_segmented) { // Shannon's diversity jsonDiversity["index_H_entropy"][code] = kv.second; - // Shannon's equitability + // Pielou's evenness J' (also known as Shannon's equitability) double nb_seg_nb_seg_m1 = nb_segmented[code] * (nb_segmented[code] - 1); jsonDiversity["index_E_equitability"][code] = index_H_entropy[code] / log(nb_segmented[code]) ; diff --git a/browser/js/tools.js b/browser/js/tools.js index 02a348204c50ddef44235db06f483659cdc2ee78..8c0a15ee36ea0c8ec247ee0da1bcdf3d2fed21fc 100644 --- a/browser/js/tools.js +++ b/browser/js/tools.js @@ -941,7 +941,7 @@ function download_csv(csv, filename) { function translate_key_diversity(key_diversity){ var table = { "index_H_entropy" : "Shannon's diversity", - "index_E_equitability" : "Shannon's equitability", + "index_E_equitability" : "Pielou's evenness", "index_Ds_diversity" : "Simpson's diversity" } return table[key_diversity] diff --git a/browser/test/QUnit/testFiles/model_test.js b/browser/test/QUnit/testFiles/model_test.js index 153c0b8f877e2df86572b094dc977546c7cb03ac..edeb4d62bab5e1540d52cb192a6c2253fea0260e 100644 --- a/browser/test/QUnit/testFiles/model_test.js +++ b/browser/test/QUnit/testFiles/model_test.js @@ -752,7 +752,7 @@ QUnit.test("getPointHtmlInfo", function(assert) { html_info = m.getPointHtmlInfo(1) // each diversity indices has header assert.includes(html_info, "Shannon's diversity") - assert.includes(html_info, "Shannon's equitability") + assert.includes(html_info, "Pielou's evenness") assert.includes(html_info, "Simpson's diversity") // each present locus id visible assert.includes(html_info, 'Simpson\'s diversity x all') diff --git a/doc/user.md b/doc/user.md index 2d44fc536b08733a2e16a45905e256cecb936bbb..b3fe52192ce365164019384d71a84f55418d958f 100644 --- a/doc/user.md +++ b/doc/user.md @@ -774,16 +774,20 @@ analyzed reads, including the hidden clonotypes. Several indices are computed on the full list of clonotypes to assess the diversity and overlap of sample(s): -- On one sample, [diversity indices](https://en.wikipedia.org/wiki/Diversity_index) such as - Shannon's diversity, Shannon's equitability and Simpson's diversity, as computed by [vijdil-algo](vidjil-algo.md#diversity-measures). - Some of these indices have values between 0 (no diversity, one clonotype clusters all analyzed reads) +- On one sample, *diversity indices* such as + [Shannon's diversity](https://en.wikipedia.org/wiki/Diversity_index#Shannon_index), + [Pielou's evenness](https://en.wikipedia.org/wiki/Species_evenness), + and [Simpson's diversity](https://en.wikipedia.org/wiki/Diversity_index#Simpson_index), + as computed by [vijdil-algo](vidjil-algo.md#diversity-measures). + Pielou's evenness and Simpson's diversity have values between 0 + (no diversity, one clonotype clusters all analyzed reads) and 1 (full diversity, each analyzed read belongs to a different clonotype). - On several samples, overlap indexes such as [Morisita's overlap index](https://en.wikipedia.org/wiki/Morisita%27s_overlap_index) having values between 0 (no overlap between the two samples) and 1 (full overlap, clonotypes in the same proportion in both samples). -Some of these indices are currently shown on the sample information panel (“🛈” next to the sample name in the info panel). +Some of these indices are shown on the sample information panel (“🛈” next to the sample name in the info panel). Contact us if you have other needs. ## Exporting the full list of clonotypes diff --git a/doc/vidjil-algo.md b/doc/vidjil-algo.md index a58123b64bfe5a105118adc525858b92573e62c3..96af1f728848dea90d5ad651daf2f4ee8b5ddcd3 100644 --- a/doc/vidjil-algo.md +++ b/doc/vidjil-algo.md @@ -679,7 +679,7 @@ Several [diversity indices](https://en.wikipedia.org/wiki/Diversity_index) are r for each germline/locus as well as for the entire data: - H (`index_H_entropy`): Shannon's diversity - - E (`index_E_equitability`): Shannon's equitability + - E (`index_E_equitability`): [Pielou's evenness J'](https://en.wikipedia.org/wiki/Species_evenness) (also known as Shannon's equitability) - Ds (`index_Ds_diversity`): Simpson's diversity E ans Ds values are between 0 (no diversity, one clone clusters all analyzed reads)