ENH: Show ranking values in feature tooltips

Closes #186.

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 ## Qurro 0.3.0
 ### Features added
+- Feature ranking values (i.e. differentials or loadings) are now shown in the
+  tooltips for individual features in the rank plot.
+  ([#186](https://github.com/biocore/qurro/issues/186))
+- Added a "Moving Pictures" tutorial.
 ### Backward-incompatible changes
 ### Bug fixes
 ### Performance enhancements
@@ -10,6 +14,8 @@
   make it clearer that the differentials used here are equivalent to those used
   in the Morton/Marotz et al. 2019 analysis
   (https://github.com/knightlab-analyses/reference-frames).
+- Various updates to Qurro's code and documentation.
+  ([#184](https://github.com/biocore/qurro/issues/184))
 
 
 ## Qurro 0.2.1 (July 10, 2019)

qurro/generate.py

@@ -275,6 +275,7 @@ def gen_rank_plot(V, ranking_ids, feature_metadata_cols):
                 ),
                 "Feature ID",
                 *feature_metadata_cols,
+                *ranking_ids,
             ],
         )
         .configure_axis(

qurro/tests/web_tests/tests/test_data_export.js

@@ -1,7 +1,7 @@
 define(["display", "mocha", "chai"], function(display, mocha, chai) {
     // Just the output from the python "matching" integration test
     // prettier-ignore
-    var rankPlotJSON = {"$schema": "https://vega.github.io/schema/vega-lite/v3.3.0.json", "autosize": {"resize": true}, "background": "#FFFFFF", "config": {"axis": {"gridColor": "#f2f2f2", "labelBound": true}, "mark": {"tooltip": null}, "view": {"height": 300, "width": 400}}, "data": {"name": "data-d5bf6e97702c9e72a67a25d194eadce5"}, "datasets": {"data-d5bf6e97702c9e72a67a25d194eadce5": [{"Feature ID": "Taxon1", "FeatureMetadata1": null, "FeatureMetadata2": null, "Intercept": 5.0, "Rank 1": 6.0, "Rank 2": 7.0, "qurro_classification": "None"}, {"Feature ID": "Taxon2", "FeatureMetadata1": null, "FeatureMetadata2": null, "Intercept": 1.0, "Rank 1": 2.0, "Rank 2": 3.0, "qurro_classification": "None"}, {"Feature ID": "Taxon3", "FeatureMetadata1": "Yeet", "FeatureMetadata2": "100", "Intercept": 4.0, "Rank 1": 5.0, "Rank 2": 6.0, "qurro_classification": "None"}, {"Feature ID": "Taxon4", "FeatureMetadata1": null, "FeatureMetadata2": null, "Intercept": 9.0, "Rank 1": 8.0, "Rank 2": 7.0, "qurro_classification": "None"}, {"Feature ID": "Taxon5", "FeatureMetadata1": "null", "FeatureMetadata2": "lol", "Intercept": 6.0, "Rank 1": 5.0, "Rank 2": 4.0, "qurro_classification": "None"}], "qurro_feature_metadata_ordering": ["FeatureMetadata1", "FeatureMetadata2"], "qurro_rank_ordering": ["Intercept", "Rank 1", "Rank 2"]}, "encoding": {"color": {"field": "qurro_classification", "scale": {"domain": ["None", "Numerator", "Denominator", "Both"], "range": ["#e0e0e0", "#f00", "#00f", "#949"]}, "title": "Log Ratio Classification", "type": "nominal"}, "tooltip": [{"field": "qurro_x", "title": "Current Ranking", "type": "quantitative"}, {"field": "qurro_classification", "title": "Log Ratio Classification", "type": "nominal"}, {"field": "Feature ID", "type": "nominal"}, {"field": "FeatureMetadata1", "type": "nominal"}, {"field": "FeatureMetadata2", "type": "nominal"}], "x": {"axis": {"labelAngle": 0, "ticks": false}, "field": "qurro_x", "scale": {"paddingInner": 0, "paddingOuter": 1, "rangeStep": 1}, "title": "Sorted Features", "type": "ordinal"}, "y": {"field": "Intercept", "type": "quantitative"}}, "mark": "bar", "selection": {"selector005": {"bind": "scales", "encodings": ["x", "y"], "type": "interval"}}, "title": "Feature Ranks", "transform": [{"sort": [{"field": "Intercept", "order": "ascending"}], "window": [{"as": "qurro_x", "op": "row_number"}]}]};
+    var rankPlotJSON = {"$schema": "https://vega.github.io/schema/vega-lite/v3.3.0.json", "autosize": {"resize": true}, "background": "#FFFFFF", "config": {"axis": {"gridColor": "#f2f2f2", "labelBound": true}, "mark": {"tooltip": null}, "view": {"height": 300, "width": 400}}, "data": {"name": "data-d5bf6e97702c9e72a67a25d194eadce5"}, "datasets": {"data-d5bf6e97702c9e72a67a25d194eadce5": [{"Feature ID": "Taxon1", "FeatureMetadata1": null, "FeatureMetadata2": null, "Intercept": 5.0, "Rank 1": 6.0, "Rank 2": 7.0, "qurro_classification": "None"}, {"Feature ID": "Taxon2", "FeatureMetadata1": null, "FeatureMetadata2": null, "Intercept": 1.0, "Rank 1": 2.0, "Rank 2": 3.0, "qurro_classification": "None"}, {"Feature ID": "Taxon3", "FeatureMetadata1": "Yeet", "FeatureMetadata2": "100", "Intercept": 4.0, "Rank 1": 5.0, "Rank 2": 6.0, "qurro_classification": "None"}, {"Feature ID": "Taxon4", "FeatureMetadata1": null, "FeatureMetadata2": null, "Intercept": 9.0, "Rank 1": 8.0, "Rank 2": 7.0, "qurro_classification": "None"}, {"Feature ID": "Taxon5", "FeatureMetadata1": "null", "FeatureMetadata2": "lol", "Intercept": 6.0, "Rank 1": 5.0, "Rank 2": 4.0, "qurro_classification": "None"}], "qurro_feature_metadata_ordering": ["FeatureMetadata1", "FeatureMetadata2"], "qurro_rank_ordering": ["Intercept", "Rank 1", "Rank 2"]}, "encoding": {"color": {"field": "qurro_classification", "scale": {"domain": ["None", "Numerator", "Denominator", "Both"], "range": ["#e0e0e0", "#f00", "#00f", "#949"]}, "title": "Log Ratio Classification", "type": "nominal"}, "tooltip": [{"field": "qurro_x", "title": "Current Ranking", "type": "quantitative"}, {"field": "qurro_classification", "title": "Log Ratio Classification", "type": "nominal"}, {"field": "Feature ID", "type": "nominal"}, {"field": "FeatureMetadata1", "type": "nominal"}, {"field": "FeatureMetadata2", "type": "nominal"}, {"field": "Intercept", "type": "quantitative"}, {"field": "Rank 1", "type": "quantitative"}, {"field": "Rank 2", "type": "quantitative"}], "x": {"axis": {"labelAngle": 0, "ticks": false}, "field": "qurro_x", "scale": {"paddingInner": 0, "paddingOuter": 1, "rangeStep": 1}, "title": "Sorted Features", "type": "ordinal"}, "y": {"field": "Intercept", "type": "quantitative"}}, "mark": "bar", "selection": {"selector005": {"bind": "scales", "encodings": ["x", "y"], "type": "interval"}}, "title": "Feature Ranks", "transform": [{"sort": [{"field": "Intercept", "order": "ascending"}], "window": [{"as": "qurro_x", "op": "row_number"}]}]};
     // prettier-ignore
     var samplePlotJSON = {"$schema": "https://vega.github.io/schema/vega-lite/v3.3.0.json", "autosize": {"resize": true}, "background": "#FFFFFF", "config": {"axis": {"labelBound": true}, "mark": {"tooltip": null}, "range": {"category": {"scheme": "tableau10"}, "ramp": {"scheme": "blues"}}, "view": {"height": 300, "width": 400}}, "data": {"name": "data-17ad6d7eb8d11fdb67d65d9f4abd5654"}, "datasets": {"data-17ad6d7eb8d11fdb67d65d9f4abd5654": [{"Metadata1": "1", "Metadata2": "2", "Metadata3": "3", "Sample ID": "Sample1", "qurro_balance": null}, {"Metadata1": "4", "Metadata2": "5", "Metadata3": "6", "Sample ID": "Sample2", "qurro_balance": null}, {"Metadata1": "7", "Metadata2": "8", "Metadata3": "9", "Sample ID": "Sample3", "qurro_balance": null}, {"Metadata1": "13", "Metadata2": "14", "Metadata3": "15", "Sample ID": "Sample5", "qurro_balance": null}, {"Metadata1": "16", "Metadata2": "17", "Metadata3": "18", "Sample ID": "Sample6", "qurro_balance": null}, {"Metadata1": "19", "Metadata2": "20", "Metadata3": "21", "Sample ID": "Sample7", "qurro_balance": null}]}, "encoding": {"color": {"field": "Metadata1", "type": "nominal"}, "tooltip": [{"field": "Sample ID", "type": "nominal"}, {"field": "qurro_balance", "type": "quantitative"}], "x": {"axis": {"labelAngle": -45}, "field": "Metadata1", "type": "nominal"}, "y": {"field": "qurro_balance", "title": "log(Numerator / Denominator)", "type": "quantitative"}}, "mark": {"type": "circle"}, "selection": {"selector006": {"bind": "scales", "encodings": ["x", "y"], "type": "interval"}}, "title": "Log Ratio of Abundances in Samples"};
     // prettier-ignore

qurro/tests/web_tests/tests/test_rrvdisplay.js

@@ -7,7 +7,7 @@ define(["display", "mocha", "chai", "testing_utilities", "dom_utils"], function(
 ) {
     // Just the output from the python "matching" integration test
     // prettier-ignore
-    var rankPlotJSON = {"$schema": "https://vega.github.io/schema/vega-lite/v3.3.0.json", "autosize": {"resize": true}, "background": "#FFFFFF", "config": {"axis": {"gridColor": "#f2f2f2", "labelBound": true}, "mark": {"tooltip": null}, "view": {"height": 300, "width": 400}}, "data": {"name": "data-d5bf6e97702c9e72a67a25d194eadce5"}, "datasets": {"data-d5bf6e97702c9e72a67a25d194eadce5": [{"Feature ID": "Taxon1", "FeatureMetadata1": null, "FeatureMetadata2": null, "Intercept": 5.0, "Rank 1": 6.0, "Rank 2": 7.0, "qurro_classification": "None"}, {"Feature ID": "Taxon2", "FeatureMetadata1": null, "FeatureMetadata2": null, "Intercept": 1.0, "Rank 1": 2.0, "Rank 2": 3.0, "qurro_classification": "None"}, {"Feature ID": "Taxon3", "FeatureMetadata1": "Yeet", "FeatureMetadata2": "100", "Intercept": 4.0, "Rank 1": 5.0, "Rank 2": 6.0, "qurro_classification": "None"}, {"Feature ID": "Taxon4", "FeatureMetadata1": null, "FeatureMetadata2": null, "Intercept": 9.0, "Rank 1": 8.0, "Rank 2": 7.0, "qurro_classification": "None"}, {"Feature ID": "Taxon5", "FeatureMetadata1": "null", "FeatureMetadata2": "lol", "Intercept": 6.0, "Rank 1": 5.0, "Rank 2": 4.0, "qurro_classification": "None"}], "qurro_feature_metadata_ordering": ["FeatureMetadata1", "FeatureMetadata2"], "qurro_rank_ordering": ["Intercept", "Rank 1", "Rank 2"]}, "encoding": {"color": {"field": "qurro_classification", "scale": {"domain": ["None", "Numerator", "Denominator", "Both"], "range": ["#e0e0e0", "#f00", "#00f", "#949"]}, "title": "Log Ratio Classification", "type": "nominal"}, "tooltip": [{"field": "qurro_x", "title": "Current Ranking", "type": "quantitative"}, {"field": "qurro_classification", "title": "Log Ratio Classification", "type": "nominal"}, {"field": "Feature ID", "type": "nominal"}, {"field": "FeatureMetadata1", "type": "nominal"}, {"field": "FeatureMetadata2", "type": "nominal"}], "x": {"axis": {"labelAngle": 0, "ticks": false}, "field": "qurro_x", "scale": {"paddingInner": 0, "paddingOuter": 1, "rangeStep": 1}, "title": "Sorted Features", "type": "ordinal"}, "y": {"field": "Intercept", "type": "quantitative"}}, "mark": "bar", "selection": {"selector005": {"bind": "scales", "encodings": ["x", "y"], "type": "interval"}}, "title": "Feature Ranks", "transform": [{"sort": [{"field": "Intercept", "order": "ascending"}], "window": [{"as": "qurro_x", "op": "row_number"}]}]};
+    var rankPlotJSON = {"$schema": "https://vega.github.io/schema/vega-lite/v3.3.0.json", "autosize": {"resize": true}, "background": "#FFFFFF", "config": {"axis": {"gridColor": "#f2f2f2", "labelBound": true}, "mark": {"tooltip": null}, "view": {"height": 300, "width": 400}}, "data": {"name": "data-d5bf6e97702c9e72a67a25d194eadce5"}, "datasets": {"data-d5bf6e97702c9e72a67a25d194eadce5": [{"Feature ID": "Taxon1", "FeatureMetadata1": null, "FeatureMetadata2": null, "Intercept": 5.0, "Rank 1": 6.0, "Rank 2": 7.0, "qurro_classification": "None"}, {"Feature ID": "Taxon2", "FeatureMetadata1": null, "FeatureMetadata2": null, "Intercept": 1.0, "Rank 1": 2.0, "Rank 2": 3.0, "qurro_classification": "None"}, {"Feature ID": "Taxon3", "FeatureMetadata1": "Yeet", "FeatureMetadata2": "100", "Intercept": 4.0, "Rank 1": 5.0, "Rank 2": 6.0, "qurro_classification": "None"}, {"Feature ID": "Taxon4", "FeatureMetadata1": null, "FeatureMetadata2": null, "Intercept": 9.0, "Rank 1": 8.0, "Rank 2": 7.0, "qurro_classification": "None"}, {"Feature ID": "Taxon5", "FeatureMetadata1": "null", "FeatureMetadata2": "lol", "Intercept": 6.0, "Rank 1": 5.0, "Rank 2": 4.0, "qurro_classification": "None"}], "qurro_feature_metadata_ordering": ["FeatureMetadata1", "FeatureMetadata2"], "qurro_rank_ordering": ["Intercept", "Rank 1", "Rank 2"]}, "encoding": {"color": {"field": "qurro_classification", "scale": {"domain": ["None", "Numerator", "Denominator", "Both"], "range": ["#e0e0e0", "#f00", "#00f", "#949"]}, "title": "Log Ratio Classification", "type": "nominal"}, "tooltip": [{"field": "qurro_x", "title": "Current Ranking", "type": "quantitative"}, {"field": "qurro_classification", "title": "Log Ratio Classification", "type": "nominal"}, {"field": "Feature ID", "type": "nominal"}, {"field": "FeatureMetadata1", "type": "nominal"}, {"field": "FeatureMetadata2", "type": "nominal"}, {"field": "Intercept", "type": "quantitative"}, {"field": "Rank 1", "type": "quantitative"}, {"field": "Rank 2", "type": "quantitative"}], "x": {"axis": {"labelAngle": 0, "ticks": false}, "field": "qurro_x", "scale": {"paddingInner": 0, "paddingOuter": 1, "rangeStep": 1}, "title": "Sorted Features", "type": "ordinal"}, "y": {"field": "Intercept", "type": "quantitative"}}, "mark": "bar", "selection": {"selector005": {"bind": "scales", "encodings": ["x", "y"], "type": "interval"}}, "title": "Feature Ranks", "transform": [{"sort": [{"field": "Intercept", "order": "ascending"}], "window": [{"as": "qurro_x", "op": "row_number"}]}]};
     // prettier-ignore
     var samplePlotJSON = {"$schema": "https://vega.github.io/schema/vega-lite/v3.3.0.json", "autosize": {"resize": true}, "background": "#FFFFFF", "config": {"axis": {"labelBound": true}, "mark": {"tooltip": null}, "range": {"category": {"scheme": "tableau10"}, "ramp": {"scheme": "blues"}}, "view": {"height": 300, "width": 400}}, "data": {"name": "data-17ad6d7eb8d11fdb67d65d9f4abd5654"}, "datasets": {"data-17ad6d7eb8d11fdb67d65d9f4abd5654": [{"Metadata1": "1", "Metadata2": "2", "Metadata3": "3", "Sample ID": "Sample1", "qurro_balance": null}, {"Metadata1": "4", "Metadata2": "5", "Metadata3": "6", "Sample ID": "Sample2", "qurro_balance": null}, {"Metadata1": "7", "Metadata2": "8", "Metadata3": "9", "Sample ID": "Sample3", "qurro_balance": null}, {"Metadata1": "13", "Metadata2": "14", "Metadata3": "15", "Sample ID": "Sample5", "qurro_balance": null}, {"Metadata1": "16", "Metadata2": "17", "Metadata3": "18", "Sample ID": "Sample6", "qurro_balance": null}, {"Metadata1": "19", "Metadata2": "20", "Metadata3": "21", "Sample ID": "Sample7", "qurro_balance": null}]}, "encoding": {"color": {"field": "Metadata1", "type": "nominal"}, "tooltip": [{"field": "Sample ID", "type": "nominal"}, {"field": "qurro_balance", "type": "quantitative"}], "x": {"axis": {"labelAngle": -45}, "field": "Metadata1", "type": "nominal"}, "y": {"field": "qurro_balance", "title": "log(Numerator / Denominator)", "type": "quantitative"}}, "mark": {"type": "circle"}, "selection": {"selector006": {"bind": "scales", "encodings": ["x", "y"], "type": "interval"}}, "title": "Log Ratio of Abundances in Samples"};
     // prettier-ignore