MAINT: generate r. plot window transform w/ Altair

Progress towards a way of implementing #46 without a bunch of crazy custom sorting code in JS. Things to do before we're done here: -modify JS code to adjust rank plot spec in the following ways on rank change: -change encoding.y field -change transform[0].sort[0].field -modify python code to completely replace rankratioviz_x with rrv_x (i.e. we're still using a field called rankratioviz_x, but now Vega-Lite is generating it for us) -remove all the unused code that this will replace :D
biocore · May 17, 2019 · fb8b838 · fb8b838
1 parent e849f1f
commit fb8b838
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Showing 3 changed files with 11 additions and 6 deletions.
diff --git a/rankratioviz/generate.py b/rankratioviz/generate.py
@@ -311,12 +311,19 @@ def gen_rank_plot(V):
             autosize=alt.AutoSizeParams(resize=True),
         )
         .mark_bar()
+        .transform_window(
+            sort=[alt.SortField(field=default_rank_col, order="ascending")],
+            # We don't use an alt.WindowFieldDef here because python gets
+            # confused when you use "as" as an actual argument name. So we just
+            # use this syntax.
+            window=[{"op": "rank", "as": "rrv_x"}],
+        )
         .encode(
             # type="ordinal" needed on the scale here to make bars adjacent;
             # see https://stackoverflow.com/a/55544817/10730311. For now, we're
             # sticking with type="quantitative" in order to allow for
             # zooming/panning along the x-axis.
-            x=alt.X("rankratioviz_x", title="Features", type="quantitative"),
+            x=alt.X("rrv_x", title="Features", type="quantitative"),
             y=alt.Y(default_rank_col, type="quantitative"),
             color=alt.Color(
                 "Classification",
@@ -328,9 +335,7 @@ def gen_rank_plot(V):
             size=alt.value(1.0),
             tooltip=[
                 alt.Tooltip(
-                    field="rankratioviz_x",
-                    title="Current Ranking",
-                    type="quantitative",
+                    field="rrv_x", title="Current Ranking", type="quantitative"
                 ),
                 "Classification",
                 "Feature ID",

diff --git a/rankratioviz/tests/web_tests/tests/test_data_export.js b/rankratioviz/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 = {"config": {"view": {"width": 400, "height": 300}, "mark": {"tooltip": null}, "axis": {"gridColor": "#f2f2f2", "labelBound": true}}, "data": {"name": "data-fd4989a380e929d595376bdbc2fa6a20"}, "mark": "bar", "autosize": {"resize": true}, "background": "#FFFFFF", "encoding": {"color": {"type": "nominal", "field": "Classification", "scale": {"domain": ["None", "Numerator", "Denominator", "Both"], "range": ["#e0e0e0", "#f00", "#00f", "#949"]}}, "size": {"value": 1.0}, "tooltip": [{"type": "quantitative", "field": "rankratioviz_x", "title": "Current Ranking"}, {"type": "nominal", "field": "Classification"}, {"type": "nominal", "field": "Feature ID"}], "x": {"type": "quantitative", "field": "rankratioviz_x", "title": "Features"}, "y": {"type": "quantitative", "field": "Intercept"}}, "selection": {"selector007": {"type": "interval", "bind": "scales", "encodings": ["x", "y"]}}, "title": "Feature Ranks", "$schema": "https://vega.github.io/schema/vega-lite/v3.2.1.json", "datasets": {"data-fd4989a380e929d595376bdbc2fa6a20": [{"Feature ID": "Taxon2", "rankratioviz_x": 0, "Classification": "None", "Intercept": 1.0, "Rank 1": 2.0, "Rank 2": 3.0}, {"Feature ID": "Taxon3|Yeet|100", "rankratioviz_x": 1, "Classification": "None", "Intercept": 4.0, "Rank 1": 5.0, "Rank 2": 6.0}, {"Feature ID": "Taxon1", "rankratioviz_x": 2, "Classification": "None", "Intercept": 5.0, "Rank 1": 6.0, "Rank 2": 7.0}, {"Feature ID": "Taxon5", "rankratioviz_x": 3, "Classification": "None", "Intercept": 6.0, "Rank 1": 5.0, "Rank 2": 4.0}, {"Feature ID": "Taxon4", "rankratioviz_x": 4, "Classification": "None", "Intercept": 9.0, "Rank 1": 8.0, "Rank 2": 7.0}], "rankratioviz_rank_ordering": ["Intercept", "Rank 1", "Rank 2"]}};
+    var rankPlotJSON = {"config": {"view": {"width": 400, "height": 300}, "mark": {"tooltip": null}, "axis": {"gridColor": "#f2f2f2", "labelBound": true}}, "data": {"name": "data-fd4989a380e929d595376bdbc2fa6a20"}, "mark": "bar", "autosize": {"resize": true}, "background": "#FFFFFF", "encoding": {"color": {"type": "nominal", "field": "Classification", "scale": {"domain": ["None", "Numerator", "Denominator", "Both"], "range": ["#e0e0e0", "#f00", "#00f", "#949"]}}, "size": {"value": 1.0}, "tooltip": [{"type": "quantitative", "field": "rrv_x", "title": "Current Ranking"}, {"type": "nominal", "field": "Classification"}, {"type": "nominal", "field": "Feature ID"}], "x": {"type": "quantitative", "field": "rrv_x", "title": "Features"}, "y": {"type": "quantitative", "field": "Intercept"}}, "selection": {"selector007": {"type": "interval", "bind": "scales", "encodings": ["x", "y"]}}, "title": "Feature Ranks", "transform": [{"window": [{"op": "rank", "as": "rrv_x"}], "sort": [{"field": "Intercept", "order": "ascending"}]}], "$schema": "https://vega.github.io/schema/vega-lite/v3.2.1.json", "datasets": {"data-fd4989a380e929d595376bdbc2fa6a20": [{"Feature ID": "Taxon2", "rankratioviz_x": 0, "Classification": "None", "Intercept": 1.0, "Rank 1": 2.0, "Rank 2": 3.0}, {"Feature ID": "Taxon3|Yeet|100", "rankratioviz_x": 1, "Classification": "None", "Intercept": 4.0, "Rank 1": 5.0, "Rank 2": 6.0}, {"Feature ID": "Taxon1", "rankratioviz_x": 2, "Classification": "None", "Intercept": 5.0, "Rank 1": 6.0, "Rank 2": 7.0}, {"Feature ID": "Taxon5", "rankratioviz_x": 3, "Classification": "None", "Intercept": 6.0, "Rank 1": 5.0, "Rank 2": 4.0}, {"Feature ID": "Taxon4", "rankratioviz_x": 4, "Classification": "None", "Intercept": 9.0, "Rank 1": 8.0, "Rank 2": 7.0}], "rankratioviz_rank_ordering": ["Intercept", "Rank 1", "Rank 2"]}};
     // prettier-ignore
     var samplePlotJSON = {"config": {"view": {"width": 400, "height": 300}, "mark": {"tooltip": null}}, "data": {"name": "data-587975575c35e2a2f0cf84839938cac8"}, "mark": "circle", "autosize": {"resize": true}, "background": "#FFFFFF", "encoding": {"color": {"type": "nominal", "field": "Metadata1"}, "tooltip": [{"type": "nominal", "field": "Sample ID"}, {"type": "quantitative", "field": "rankratioviz_balance"}], "x": {"type": "quantitative", "field": "rankratioviz_balance"}, "y": {"type": "quantitative", "field": "rankratioviz_balance", "title": "log(Numerator / Denominator)"}}, "title": "Log Ratio of Abundances in Samples", "$schema": "https://vega.github.io/schema/vega-lite/v3.2.1.json", "datasets": {"data-587975575c35e2a2f0cf84839938cac8": [{"Sample ID": "Sample1", "rankratioviz_balance": null, "Metadata1": 1, "Metadata2": 2, "Metadata3": 3}, {"Sample ID": "Sample2", "rankratioviz_balance": null, "Metadata1": 4, "Metadata2": 5, "Metadata3": 6}, {"Sample ID": "Sample3", "rankratioviz_balance": null, "Metadata1": 7, "Metadata2": 8, "Metadata3": 9}, {"Sample ID": "Sample5", "rankratioviz_balance": null, "Metadata1": 13, "Metadata2": 14, "Metadata3": 15}, {"Sample ID": "Sample6", "rankratioviz_balance": null, "Metadata1": 16, "Metadata2": 17, "Metadata3": 18}, {"Sample ID": "Sample7", "rankratioviz_balance": null, "Metadata1": 19, "Metadata2": 20, "Metadata3": 21}]}};
     // prettier-ignore

diff --git a/rankratioviz/tests/web_tests/tests/test_rrvdisplay.js b/rankratioviz/tests/web_tests/tests/test_rrvdisplay.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 = {"config": {"view": {"width": 400, "height": 300}, "mark": {"tooltip": null}, "axis": {"gridColor": "#f2f2f2", "labelBound": true}}, "data": {"name": "data-fd4989a380e929d595376bdbc2fa6a20"}, "mark": "bar", "autosize": {"resize": true}, "background": "#FFFFFF", "encoding": {"color": {"type": "nominal", "field": "Classification", "scale": {"domain": ["None", "Numerator", "Denominator", "Both"], "range": ["#e0e0e0", "#f00", "#00f", "#949"]}}, "size": {"value": 1.0}, "tooltip": [{"type": "quantitative", "field": "rankratioviz_x", "title": "Current Ranking"}, {"type": "nominal", "field": "Classification"}, {"type": "nominal", "field": "Feature ID"}], "x": {"type": "quantitative", "field": "rankratioviz_x", "title": "Features"}, "y": {"type": "quantitative", "field": "Intercept"}}, "selection": {"selector007": {"type": "interval", "bind": "scales", "encodings": ["x", "y"]}}, "title": "Feature Ranks", "$schema": "https://vega.github.io/schema/vega-lite/v3.2.1.json", "datasets": {"data-fd4989a380e929d595376bdbc2fa6a20": [{"Feature ID": "Taxon2", "rankratioviz_x": 0, "Classification": "None", "Intercept": 1.0, "Rank 1": 2.0, "Rank 2": 3.0}, {"Feature ID": "Taxon3|Yeet|100", "rankratioviz_x": 1, "Classification": "None", "Intercept": 4.0, "Rank 1": 5.0, "Rank 2": 6.0}, {"Feature ID": "Taxon1", "rankratioviz_x": 2, "Classification": "None", "Intercept": 5.0, "Rank 1": 6.0, "Rank 2": 7.0}, {"Feature ID": "Taxon5", "rankratioviz_x": 3, "Classification": "None", "Intercept": 6.0, "Rank 1": 5.0, "Rank 2": 4.0}, {"Feature ID": "Taxon4", "rankratioviz_x": 4, "Classification": "None", "Intercept": 9.0, "Rank 1": 8.0, "Rank 2": 7.0}], "rankratioviz_rank_ordering": ["Intercept", "Rank 1", "Rank 2"]}};
+    var rankPlotJSON = {"config": {"view": {"width": 400, "height": 300}, "mark": {"tooltip": null}, "axis": {"gridColor": "#f2f2f2", "labelBound": true}}, "data": {"name": "data-fd4989a380e929d595376bdbc2fa6a20"}, "mark": "bar", "autosize": {"resize": true}, "background": "#FFFFFF", "encoding": {"color": {"type": "nominal", "field": "Classification", "scale": {"domain": ["None", "Numerator", "Denominator", "Both"], "range": ["#e0e0e0", "#f00", "#00f", "#949"]}}, "size": {"value": 1.0}, "tooltip": [{"type": "quantitative", "field": "rrv_x", "title": "Current Ranking"}, {"type": "nominal", "field": "Classification"}, {"type": "nominal", "field": "Feature ID"}], "x": {"type": "quantitative", "field": "rrv_x", "title": "Features"}, "y": {"type": "quantitative", "field": "Intercept"}}, "selection": {"selector007": {"type": "interval", "bind": "scales", "encodings": ["x", "y"]}}, "title": "Feature Ranks", "transform": [{"window": [{"op": "rank", "as": "rrv_x"}], "sort": [{"field": "Intercept", "order": "ascending"}]}], "$schema": "https://vega.github.io/schema/vega-lite/v3.2.1.json", "datasets": {"data-fd4989a380e929d595376bdbc2fa6a20": [{"Feature ID": "Taxon2", "rankratioviz_x": 0, "Classification": "None", "Intercept": 1.0, "Rank 1": 2.0, "Rank 2": 3.0}, {"Feature ID": "Taxon3|Yeet|100", "rankratioviz_x": 1, "Classification": "None", "Intercept": 4.0, "Rank 1": 5.0, "Rank 2": 6.0}, {"Feature ID": "Taxon1", "rankratioviz_x": 2, "Classification": "None", "Intercept": 5.0, "Rank 1": 6.0, "Rank 2": 7.0}, {"Feature ID": "Taxon5", "rankratioviz_x": 3, "Classification": "None", "Intercept": 6.0, "Rank 1": 5.0, "Rank 2": 4.0}, {"Feature ID": "Taxon4", "rankratioviz_x": 4, "Classification": "None", "Intercept": 9.0, "Rank 1": 8.0, "Rank 2": 7.0}], "rankratioviz_rank_ordering": ["Intercept", "Rank 1", "Rank 2"]}};
     // prettier-ignore
     var samplePlotJSON = {"config": {"view": {"width": 400, "height": 300}, "mark": {"tooltip": null}}, "data": {"name": "data-587975575c35e2a2f0cf84839938cac8"}, "mark": "circle", "autosize": {"resize": true}, "background": "#FFFFFF", "encoding": {"color": {"type": "nominal", "field": "Metadata1"}, "tooltip": [{"type": "nominal", "field": "Sample ID"}, {"type": "quantitative", "field": "rankratioviz_balance"}], "x": {"type": "quantitative", "field": "rankratioviz_balance"}, "y": {"type": "quantitative", "field": "rankratioviz_balance", "title": "log(Numerator / Denominator)"}}, "title": "Log Ratio of Abundances in Samples", "$schema": "https://vega.github.io/schema/vega-lite/v3.2.1.json", "datasets": {"data-587975575c35e2a2f0cf84839938cac8": [{"Sample ID": "Sample1", "rankratioviz_balance": null, "Metadata1": 1, "Metadata2": 2, "Metadata3": 3}, {"Sample ID": "Sample2", "rankratioviz_balance": null, "Metadata1": 4, "Metadata2": 5, "Metadata3": 6}, {"Sample ID": "Sample3", "rankratioviz_balance": null, "Metadata1": 7, "Metadata2": 8, "Metadata3": 9}, {"Sample ID": "Sample5", "rankratioviz_balance": null, "Metadata1": 13, "Metadata2": 14, "Metadata3": 15}, {"Sample ID": "Sample6", "rankratioviz_balance": null, "Metadata1": 16, "Metadata2": 17, "Metadata3": 18}, {"Sample ID": "Sample7", "rankratioviz_balance": null, "Metadata1": 19, "Metadata2": 20, "Metadata3": 21}]}};
     // prettier-ignore