Small viz improvements (#21)

* Update config viz * Syntax replace not by is None * Fix test randomness
aphp · Jul 28, 2023 · 0ca0b9c · 0ca0b9c
1 parent 2babbc5
commit 0ca0b9c
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Showing 50 changed files with 547 additions and 495 deletions.
diff --git a/edsteva/io/synthetic/note.py b/edsteva/io/synthetic/note.py
@@ -55,7 +55,7 @@ def _generate_note_step(
 ):
     t_end = visit_care_site[date_col].max()
     t0 = generator.integers(t0_visit, t_end)
-    c_before = generator.uniform(0, 0.2)
+    c_before = generator.uniform(0, 0.01)
     c_after = generator.uniform(0.8, 1)
     note_before_t0_visit = (
         visit_care_site[visit_care_site[date_col] <= t0_visit][[id_visit_col, date_col]]

diff --git a/edsteva/io/synthetic/synthetic.py b/edsteva/io/synthetic/synthetic.py
@@ -174,6 +174,7 @@ def __post_init__(self):
 
     def generate(self):
         if self.seed:
+            np.random.seed(self.seed)
             self.generator = np.random.default_rng(self.seed)
         else:
             self.generator = np.random.default_rng()
@@ -630,7 +631,10 @@ def _generate_measurement(
                 ]
                 measurement[self.id_visit_col] = (
                     visit_care_site[self.id_visit_col]
-                    .sample(n=measurement.shape[0], replace=True)
+                    .sample(
+                        n=measurement.shape[0],
+                        replace=True,
+                    )
                     .reset_index(drop=True)
                 )
                 measurement["value_as_number"] = [None] * missing_value + list(

diff --git a/edsteva/models/rectangle_function/viz_configs/defaults.py b/edsteva/models/rectangle_function/viz_configs/defaults.py
@@ -69,6 +69,7 @@ def get_t_1_selection(predictor: DataFrame):
 
 
 normalized_probe_line = dict(
+    legend_title="Mean",
     encode=dict(
         strokeDash=alt.StrokeDash(
             "legend_predictor",
@@ -81,7 +82,7 @@ def get_t_1_selection(predictor: DataFrame):
                 orient="top",
             ),
         )
-    )
+    ),
 )
 probe_line = dict(
     encode=dict(
@@ -155,6 +156,25 @@ def get_t_1_selection(predictor: DataFrame):
     filters=[dict(filter=alt.datum.t_0 == alt.datum.max_t0)],
 )
 
+error_line = dict(
+    legend_title="Standard deviation",
+    mark_errorband=dict(
+        extent="stdev",
+    ),
+    encode=dict(
+        stroke=alt.Stroke(
+            "legend_error_band",
+            title="Error band",
+            legend=alt.Legend(
+                symbolType="square",
+                orient="top",
+                labelFontSize=12,
+                labelFontStyle="bold",
+            ),
+        ),
+    ),
+)
+
 horizontal_min_c0 = dict(
     x=alt.X(
         "min(c_0):Q",

diff --git a/edsteva/models/rectangle_function/viz_configs/normalized_probe_dashboard.py b/edsteva/models/rectangle_function/viz_configs/normalized_probe_dashboard.py
@@ -1,6 +1,7 @@
 from edsteva.utils.typing import DataFrame
 
 from .defaults import (
+    error_line,
     get_c_0_min_selection,
     get_error_max_selection,
     get_t_0_selection,
@@ -30,6 +31,7 @@ def get_normalized_probe_dashboard_config(self, predictor: DataFrame):
             c_0_min_filter,
             error_max_filter,
         ],
+        error_line=error_line,
         probe_line=normalized_probe_line,
         model_line=normalized_model_line,
         extra_horizontal_bar_charts=[horizontal_min_c0, horizontal_max_error],

diff --git a/edsteva/models/rectangle_function/viz_configs/normalized_probe_plot.py b/edsteva/models/rectangle_function/viz_configs/normalized_probe_plot.py
@@ -1,6 +1,7 @@
 from edsteva.utils.typing import DataFrame
 
 from .defaults import (
+    error_line,
     get_c_0_min_selection,
     get_error_max_selection,
     get_t_0_selection,
@@ -28,6 +29,7 @@ def get_normalized_probe_plot_config(self, predictor: DataFrame):
             c_0_min_filter,
             error_max_filter,
         ],
-        probe_line=normalized_probe_line,
+        error_line=error_line,
         model_line=normalized_model_line,
+        probe_line=normalized_probe_line,
     )
diff --git a/edsteva/models/step_function/viz_configs/defaults.py b/edsteva/models/step_function/viz_configs/defaults.py
@@ -54,6 +54,7 @@ def get_t_0_selection(predictor: DataFrame):
 
 
 normalized_probe_line = dict(
+    legend_title="Mean",
     encode=dict(
         strokeDash=alt.StrokeDash(
             "legend_predictor",
@@ -66,8 +67,9 @@ def get_t_0_selection(predictor: DataFrame):
                 orient="top",
             ),
         )
-    )
+    ),
 )
+
 probe_line = dict(
     encode=dict(
         strokeDash=alt.StrokeDash(
@@ -83,6 +85,7 @@ def get_t_0_selection(predictor: DataFrame):
         )
     )
 )
+
 normalized_model_line = dict(
     mark_line=dict(
         color="black",
@@ -140,6 +143,25 @@ def get_t_0_selection(predictor: DataFrame):
     filters=[dict(filter=alt.datum.t_0 == alt.datum.max_t0)],
 )
 
+error_line = dict(
+    legend_title="Standard deviation",
+    mark_errorband=dict(
+        extent="stdev",
+    ),
+    encode=dict(
+        stroke=alt.Stroke(
+            "legend_error_band",
+            title="Error band",
+            legend=alt.Legend(
+                symbolType="square",
+                orient="top",
+                labelFontSize=12,
+                labelFontStyle="bold",
+            ),
+        ),
+    ),
+)
+
 horizontal_min_c0 = dict(
     x=alt.X(
         "min(c_0):Q",

diff --git a/edsteva/models/step_function/viz_configs/normalized_probe_dashboard.py b/edsteva/models/step_function/viz_configs/normalized_probe_dashboard.py
@@ -1,6 +1,7 @@
 from edsteva.utils.typing import DataFrame
 
 from .defaults import (
+    error_line,
     get_c_0_min_selection,
     get_error_max_selection,
     get_t_0_selection,
@@ -18,6 +19,7 @@ def get_normalized_probe_dashboard_config(self, predictor: DataFrame):
     return dict(
         estimates_selections=[c_0_min_selection, t_0_selection, error_max_selection],
         estimates_filters=[c_0_min_filter, t_0_min_filter, error_max_filter],
+        error_line=error_line,
         probe_line=normalized_probe_line,
         model_line=normalized_model_line,
         extra_horizontal_bar_charts=[horizontal_min_c0, horizontal_max_error],

diff --git a/edsteva/models/step_function/viz_configs/normalized_probe_plot.py b/edsteva/models/step_function/viz_configs/normalized_probe_plot.py
@@ -1,6 +1,7 @@
 from edsteva.utils.typing import DataFrame
 
 from .defaults import (
+    error_line,
     get_c_0_min_selection,
     get_error_max_selection,
     get_t_0_selection,
@@ -16,6 +17,7 @@ def get_normalized_probe_plot_config(self, predictor: DataFrame):
     return dict(
         estimates_selections=[c_0_min_selection, t_0_selection, error_max_selection],
         estimates_filters=[c_0_min_filter, t_0_min_filter, error_max_filter],
+        error_line=error_line,
         probe_line=normalized_probe_line,
         model_line=normalized_model_line,
     )
diff --git a/edsteva/probes/biology/viz_configs/n_measurement/defaults.py b/edsteva/probes/biology/viz_configs/n_measurement/defaults.py
@@ -124,7 +124,6 @@ def get_horizontal_bar_charts(standard_terminologies: List[str]):
 )
 
 normalized_main_chart = dict(
-    legend_title="Mean",
     encode=dict(
         x=alt.X(
             "normalized_date:Q",

diff --git a/edsteva/probes/biology/viz_configs/n_measurement/normalized_probe_dashboard.py b/edsteva/probes/biology/viz_configs/n_measurement/normalized_probe_dashboard.py
@@ -1,6 +1,5 @@
 from .defaults import (
     chart_style,
-    error_line,
     get_horizontal_bar_charts,
     normalized_main_chart,
     normalized_time_line,
@@ -16,7 +15,6 @@ def get_normalized_probe_dashboard_config(self):
         chart_style=chart_style,
         main_chart=normalized_main_chart,
         time_line=normalized_time_line,
-        error_line=error_line,
         vertical_bar_charts=vertical_bar_charts,
         horizontal_bar_charts=horizontal_bar_charts,
     )
diff --git a/edsteva/probes/biology/viz_configs/n_measurement/normalized_probe_plot.py b/edsteva/probes/biology/viz_configs/n_measurement/normalized_probe_plot.py
@@ -1,9 +1,8 @@
-from .defaults import chart_style, error_line, normalized_main_chart
+from .defaults import chart_style, normalized_main_chart
 
 
 def get_normalized_probe_plot_config(self):
     return dict(
         chart_style=chart_style,
         main_chart=normalized_main_chart,
-        error_line=error_line,
     )
diff --git a/edsteva/probes/biology/viz_configs/per_measurement/defaults.py b/edsteva/probes/biology/viz_configs/per_measurement/defaults.py
@@ -104,7 +104,7 @@ def get_horizontal_bar_charts(standard_terminologies: List[str]):
         ),
     ],
     calculates=[
-        dict(completeness=alt.datum.sum_measurement / alt.datum.max_measurement),
+        dict(c=alt.datum.sum_measurement / alt.datum.max_measurement),
     ],
     encode=dict(
         x=alt.X(
@@ -113,7 +113,7 @@ def get_horizontal_bar_charts(standard_terminologies: List[str]):
             axis=alt.Axis(tickCount="month", labelAngle=0, grid=True),
         ),
         y=alt.Y(
-            "completeness:Q",
+            "c:Q",
             title="Completeness predictor c(t)",
             axis=alt.Axis(grid=True),
         ),
@@ -125,7 +125,7 @@ def get_horizontal_bar_charts(standard_terminologies: List[str]):
         tooltip=[
             alt.Tooltip("value:N", title="Index"),
             alt.Tooltip("yearmonth(date):T", title="Date"),
-            alt.Tooltip("completeness:Q", title="c(t)", format=".2f"),
+            alt.Tooltip("c:Q", title="c(t)", format=".2f"),
         ],
     ),
     properties=dict(
@@ -135,7 +135,6 @@ def get_horizontal_bar_charts(standard_terminologies: List[str]):
 )
 
 normalized_main_chart = dict(
-    legend_title="Mean",
     encode=dict(
         x=alt.X(
             "normalized_date:Q",

diff --git a/edsteva/probes/biology/viz_configs/per_measurement/normalized_probe_dashboard.py b/edsteva/probes/biology/viz_configs/per_measurement/normalized_probe_dashboard.py
@@ -1,6 +1,5 @@
 from .defaults import (
     chart_style,
-    error_line,
     get_horizontal_bar_charts,
     normalized_main_chart,
     normalized_time_line,
@@ -16,7 +15,6 @@ def get_normalized_probe_dashboard_config(self):
         chart_style=chart_style,
         main_chart=normalized_main_chart,
         time_line=normalized_time_line,
-        error_line=error_line,
         vertical_bar_charts=vertical_bar_charts,
         horizontal_bar_charts=horizontal_bar_charts,
     )
diff --git a/edsteva/probes/biology/viz_configs/per_measurement/normalized_probe_plot.py b/edsteva/probes/biology/viz_configs/per_measurement/normalized_probe_plot.py
@@ -1,9 +1,8 @@
-from .defaults import chart_style, error_line, normalized_main_chart
+from .defaults import chart_style, normalized_main_chart
 
 
 def get_normalized_probe_plot_config(self):
     return dict(
         chart_style=chart_style,
         main_chart=normalized_main_chart,
-        error_line=error_line,
     )
diff --git a/edsteva/probes/biology/viz_configs/per_visit/defaults.py b/edsteva/probes/biology/viz_configs/per_visit/defaults.py
@@ -104,7 +104,7 @@ def get_horizontal_bar_charts(standard_terminologies: List[str]):
         ),
     ],
     calculates=[
-        dict(completeness=alt.datum.sum_visit_with_measurement / alt.datum.sum_visit),
+        dict(c=alt.datum.sum_visit_with_measurement / alt.datum.sum_visit),
     ],
     encode=dict(
         x=alt.X(
@@ -113,7 +113,7 @@ def get_horizontal_bar_charts(standard_terminologies: List[str]):
             axis=alt.Axis(tickCount="month", labelAngle=0, grid=True),
         ),
         y=alt.Y(
-            "completeness:Q",
+            "c:Q",
             title="Completeness predictor c(t)",
             axis=alt.Axis(grid=True),
         ),
@@ -125,7 +125,7 @@ def get_horizontal_bar_charts(standard_terminologies: List[str]):
         tooltip=[
             alt.Tooltip("value:N", title="Index"),
             alt.Tooltip("yearmonth(date):T", title="Date"),
-            alt.Tooltip("completeness:Q", title="c(t)", format=".2f"),
+            alt.Tooltip("c:Q", title="c(t)", format=".2f"),
         ],
     ),
     properties=dict(
@@ -135,7 +135,6 @@ def get_horizontal_bar_charts(standard_terminologies: List[str]):
 )
 
 normalized_main_chart = dict(
-    legend_title="Mean",
     encode=dict(
         x=alt.X(
             "normalized_date:Q",

diff --git a/edsteva/probes/biology/viz_configs/per_visit/normalized_probe_dashboard.py b/edsteva/probes/biology/viz_configs/per_visit/normalized_probe_dashboard.py
@@ -1,6 +1,5 @@
 from .defaults import (
     chart_style,
-    error_line,
     get_horizontal_bar_charts,
     normalized_main_chart,
     normalized_time_line,
@@ -16,7 +15,6 @@ def get_normalized_probe_dashboard_config(self):
         chart_style=chart_style,
         main_chart=normalized_main_chart,
         time_line=normalized_time_line,
-        error_line=error_line,
         vertical_bar_charts=vertical_bar_charts,
         horizontal_bar_charts=horizontal_bar_charts,
     )
diff --git a/edsteva/probes/biology/viz_configs/per_visit/normalized_probe_plot.py b/edsteva/probes/biology/viz_configs/per_visit/normalized_probe_plot.py
@@ -1,9 +1,8 @@
-from .defaults import chart_style, error_line, normalized_main_chart
+from .defaults import chart_style, normalized_main_chart
 
 
 def get_normalized_probe_plot_config(self):
     return dict(
         chart_style=chart_style,
         main_chart=normalized_main_chart,
-        error_line=error_line,
     )
diff --git a/edsteva/probes/condition/viz_configs/n_condition/defaults.py b/edsteva/probes/condition/viz_configs/n_condition/defaults.py
@@ -98,7 +98,6 @@
 )
 
 normalized_main_chart = dict(
-    legend_title="Mean",
     encode=dict(
         x=alt.X(
             "normalized_date:Q",

diff --git a/edsteva/probes/condition/viz_configs/n_condition/normalized_probe_dashboard.py b/edsteva/probes/condition/viz_configs/n_condition/normalized_probe_dashboard.py
@@ -1,6 +1,5 @@
 from .defaults import (
     chart_style,
-    error_line,
     horizontal_bar_charts,
     normalized_main_chart,
     normalized_time_line,
@@ -13,7 +12,6 @@ def get_normalized_probe_dashboard_config(self):
         chart_style=chart_style,
         main_chart=normalized_main_chart,
         time_line=normalized_time_line,
-        error_line=error_line,
         vertical_bar_charts=vertical_bar_charts,
         horizontal_bar_charts=horizontal_bar_charts,
     )
diff --git a/edsteva/probes/condition/viz_configs/n_condition/normalized_probe_plot.py b/edsteva/probes/condition/viz_configs/n_condition/normalized_probe_plot.py
@@ -1,9 +1,8 @@
-from .defaults import chart_style, error_line, normalized_main_chart
+from .defaults import chart_style, normalized_main_chart
 
 
 def get_normalized_probe_plot_config(self):
     return dict(
         chart_style=chart_style,
         main_chart=normalized_main_chart,
-        error_line=error_line,
     )