Implementation of population frequencies with selection1d stream and …

…fake frequency data

tsqc/model.py

@@ -376,6 +376,9 @@ def mutations_df(self):
                 "num_descendants": counts.num_descendants,
                 "num_inheritors": counts.num_inheritors,
                 "num_parents": counts.num_parents,
+                "Pop_A": np.random.randint(0, 20, ts.num_mutations),
+                "Pop_B": np.random.randint(0, 20, ts.num_mutations),
+                "Pop_C": np.random.randint(0, 20, ts.num_mutations),
             }
         )
 
@@ -391,6 +394,9 @@ def mutations_df(self):
                 "num_descendants": "int",
                 "num_inheritors": "int",
                 "num_parents": "int",
+                "Pop_A": "int",
+                "Pop_B": "int",
+                "Pop_C": "int",
             }
         )
 

tsqc/pages/mutations.py

@@ -15,12 +15,13 @@
 
 def make_muts_panel(log_y, tsm):
     plot_width = 1000
+    muts_df = tsm.mutations_df
     y_dim = "time"
     if log_y:
-        tsm.mutations_df["log_time"] = np.log10(1 + tsm.mutations_df["time"])
+        muts_df["log_time"] = np.log10(1 + tsm.mutations_df["time"])
         y_dim = "log_time"
 
-    points = tsm.mutations_df.hvplot.scatter(
+    points = muts_df.hvplot.scatter(
         x="position",
         y=y_dim,
         hover_cols=["id", "num_parents", "num_descendants", "num_inheritors"],
@@ -31,9 +32,8 @@ def make_muts_panel(log_y, tsm):
     )
 
     range_stream = hv.streams.RangeXY(source=points)
-    streams = [range_stream]
 
-    filtered = points.apply(filter_points, streams=streams)
+    filtered = points.apply(filter_points, streams=[range_stream])
 
     tooltips = [
         ("ID", "@id"),
@@ -46,25 +46,25 @@ def make_muts_panel(log_y, tsm):
         color="num_inheritors",
         alpha="num_inheritors",
         colorbar=True,
-        cmap="BuGn",
+        cmap="kgy",
         colorbar_position="left",
         clabel="inheritors",
-        tools=[hover],
+        tools=[hover, "tap"],
     )
 
     hover = filtered.apply(hover_points)
-    shaded = hd.datashade(filtered, width=400, height=400, streams=streams)
+    shaded = hd.datashade(filtered, width=400, height=400, streams=[range_stream])
 
     main = (shaded * hover).opts(
         hv.opts.Points(tools=["hover"], alpha=0.1, hover_alpha=0.2, size=10),
     )
 
     time_hist = hv.DynamicMap(
-        make_hist_on_axis(dimension=y_dim, points=points), streams=streams
+        make_hist_on_axis(dimension=y_dim, points=points), streams=[range_stream]
     )
     site_hist = hv.DynamicMap(
         make_hist_on_axis(dimension="position", points=points),
-        streams=streams,
+        streams=[range_stream],
     )
 
     breakpoints = tsm.ts.breakpoints(as_array=True)
@@ -76,7 +76,7 @@ def make_muts_panel(log_y, tsm):
             "y1": tsm.mutations_df[y_dim].max(),
         }
     )
-    trees_hist = hv.DynamicMap(selected_hist(bp_df), streams=streams)
+    trees_hist = hv.DynamicMap(selected_hist(bp_df), streams=[range_stream])
     trees_hist.opts(
         width=config.PLOT_WIDTH,
         height=100,
@@ -102,6 +102,41 @@ def make_muts_panel(log_y, tsm):
         annot_track = make_annotation_plot(tsm, genes_df)
         layout += annot_track
 
+    selection_stream = hv.streams.Selection1D(source=points)
+    pops = ["Pop_A", "Pop_B", "Pop_C"]
+
+    def update_pop_freq_plot(index):
+        if not index:
+            return hv.Bars([], kdims="pop", vdims="freq").opts(
+                width=config.PLOT_WIDTH, height=400, title="Tap on a mutation"
+            )
+        mut_data = muts_df.loc[index[0]]
+        freqs = mut_data[pops].values
+        bars = hv.Bars(zip(pops, freqs), "pop", "freq").opts(
+            width=config.PLOT_WIDTH,
+            height=400,
+            framewise=True,
+            title=f"Mutation {index[0]}",
+            ylim=(0, 20),
+        )
+        return bars
+
+    def update_mut_info_table(index):
+        if not index:
+            return hv.Table([], kdims=["info"], vdims=["value"]).opts(
+                width=config.PLOT_WIDTH, title="Tap on a mutation"
+            )
+        mut_data = muts_df.loc[index[0]].drop(pops)
+        return hv.Table(mut_data.items(), kdims=["info"], vdims=["value"]).opts(
+            width=config.PLOT_WIDTH, title=f"Mutation {index[0]}"
+        )
+
+    pop_data_dynamic = hv.DynamicMap(update_pop_freq_plot, streams=[selection_stream])
+    mut_info_table_dynamic = hv.DynamicMap(
+        update_mut_info_table, streams=[selection_stream]
+    )
+    layout += (pop_data_dynamic + mut_info_table_dynamic).cols(2)
+
     return pn.Column(layout.opts(shared_axes=True).cols(1))
 
 
@@ -148,4 +183,5 @@ def page(tsm):
         pn.pane.Markdown("### Plot Options"),
         log_y_checkbox,
     )
+
     return pn.Column(plot_options, muts_panel)