show parameters in plot page & download

alphastats/gui/pages/04_Analysis.py

@@ -51,7 +51,7 @@
     method = st.selectbox(
         "Analysis",
         options=["<select>"]
-        + ["------- plots -------"]
+        + ["------- plots ------------"]
         + plotting_options
         + ["------- statistics -------"]
         + statistic_options,
@@ -64,15 +64,15 @@
         show_plot = analysis_result is not None
 
     elif method in statistic_options:
-        analysis_result, *_ = gather_parameters_and_do_analysis(
+        analysis_result, _, parameters = gather_parameters_and_do_analysis(
             method,
         )
         show_df = analysis_result is not None
 
 with c2:
     # --- SHOW PLOT -------------------------------------------------------
     if show_plot:
-        display_plot(method, analysis_result)
+        display_plot(method, analysis_result, parameters)
 
     # --- SHOW STATISTICAL ANALYSIS -------------------------------------------------------
     elif show_df:

alphastats/gui/pages/06_Results.py

@@ -21,9 +21,11 @@
 
     method = saved_item[0]
     plot = saved_item[1]
+    parameters = saved_item[2]
 
     st.markdown("\n\n\n")
     st.markdown(f"#### {method}")
+    st.write(f"Parameters used for analysis: {parameters}")
 
     if st.button("x remove analysis", key="remove" + method + str(count)):
         st.session_state[StateKeys.PLOT_LIST].remove(saved_item)

alphastats/gui/utils/analysis.py

@@ -54,7 +54,7 @@ def do_analysis(self):
         if not self._works_with_nans and self._dataset.mat.isnull().values.any():
             st.error("This analysis does not work with NaN values.")
             st.stop()
-        return self._do_analysis()
+        return *self._do_analysis(), dict(self._parameters)
 
     @abstractmethod
     def _do_analysis(self):
@@ -173,7 +173,7 @@ def _do_analysis(self):
             method=self._parameters["method"],
             group=self._parameters["group"],
         )
-        return intensity_plot, None, self._parameters
+        return intensity_plot, None
 
 
 class SampleDistributionPlot(AbstractIntensityPlot, ABC):
@@ -185,7 +185,7 @@ def _do_analysis(self):
             method=self._parameters["method"],
             color=self._parameters["group"],  # no typo
         )
-        return intensity_plot, None, self._parameters
+        return intensity_plot, None
 
 
 class PCAPlotAnalysis(AbstractDimensionReductionAnalysis):
@@ -198,7 +198,7 @@ def _do_analysis(self):
             group=self._parameters["group"],
             circle=self._parameters["circle"],
         )
-        return pca_plot, None, self._parameters
+        return pca_plot, None
 
 
 class UMAPPlotAnalysis(AbstractDimensionReductionAnalysis):
@@ -210,7 +210,7 @@ def _do_analysis(self):
             group=self._parameters["group"],
             circle=self._parameters["circle"],
         )
-        return umap_plot, None, self._parameters
+        return umap_plot, None
 
 
 class TSNEPlotAnalysis(AbstractDimensionReductionAnalysis):
@@ -242,7 +242,7 @@ def _do_analysis(self):
             perplexity=self._parameters["perplexity"],
             n_iter=self._parameters["n_iter"],
         )
-        return tsne_plot, None, self._parameters
+        return tsne_plot, None
 
 
 class VolcanoPlotAnalysis(AbstractGroupCompareAnalysis):
@@ -308,7 +308,7 @@ def _do_analysis(self):
             fdr=self._parameters["fdr"],
             color_list=self._parameters["color_list"],
         )
-        return volcano_plot.plot, volcano_plot, self._parameters
+        return volcano_plot.plot, volcano_plot
 
 
 class ClustermapAnalysis(AbstractAnalysis):
@@ -319,7 +319,7 @@ class ClustermapAnalysis(AbstractAnalysis):
     def _do_analysis(self):
         """Draw Clustermap using the Clustermap class."""
         clustermap = self._dataset.plot_clustermap()
-        return clustermap, None, self._parameters
+        return clustermap, None
 
 
 class DendrogramAnalysis(AbstractAnalysis):
@@ -330,7 +330,7 @@ class DendrogramAnalysis(AbstractAnalysis):
     def _do_analysis(self):
         """Draw Clustermap using the Clustermap class."""
         dendrogram = self._dataset.plot_dendrogram()
-        return dendrogram, None, self._parameters
+        return dendrogram, None
 
 
 class DifferentialExpressionAnalysis(AbstractGroupCompareAnalysis):
@@ -359,7 +359,7 @@ def _do_analysis(self):
             group2=self._parameters["group2"],
             column=self._parameters["column"],
         )
-        return diff_exp_analysis, None, self._parameters
+        return diff_exp_analysis, None
 
 
 class TukeyTestAnalysis(AbstractAnalysis):
@@ -384,7 +384,7 @@ def _do_analysis(self):
             protein_id=self._parameters["protein_id"],
             group=self._parameters["group"],
         )
-        return tukey_test_analysis, None, self._parameters
+        return tukey_test_analysis, None
 
 
 class AnovaAnalysis(AbstractGroupCompareAnalysis):
@@ -415,7 +415,7 @@ def _do_analysis(self):
             protein_ids=self._parameters["protein_ids"],
             tukey=self._parameters["tukey"],
         )
-        return anova_analysis, None, self._parameters
+        return anova_analysis, None
 
 
 class AncovaAnalysis(AbstractAnalysis):
@@ -448,7 +448,7 @@ def _do_analysis(self):
             covar=self._parameters["covar"],
             between=self._parameters["between"],
         )
-        return ancova_analysis, None, self._parameters
+        return ancova_analysis, None
 
 
 ANALYSIS_OPTIONS = {

alphastats/gui/utils/analysis_helper.py

@@ -18,39 +18,35 @@ def display_figure(plot):
         st.pyplot(plot)
 
 
-def save_plot_to_session_state(method, plot):
-    """
-    save plot with method to session state to retrieve old results
-    """
-    st.session_state[StateKeys.PLOT_LIST] += [(method, plot)]
-
-
-def display_df(df):
-    mask = df.applymap(type) != bool  # noqa: E721
-    d = {True: "TRUE", False: "FALSE"}
-    df = df.where(mask, df.replace(d))
-    st.dataframe(df)
-
-
 @st.fragment
-def display_plot(method, analysis_result, show_save_button=True) -> None:
+def display_plot(
+    method: str,
+    analysis_result: Any,
+    parameters: Optional[Dict] = None,
+    show_save_button=True,
+) -> None:
     """A fragment to display the plot and download options."""
     display_figure(analysis_result)
 
     c1, c2, c3 = st.columns([1, 1, 1])
 
     with c1:
         if show_save_button and st.button("Save to results page.."):
-            save_plot_to_session_state(method, analysis_result)
+            save_plot_to_session_state(method, analysis_result, parameters)
 
     with c2:
         download_figure(method, analysis_result, format="pdf")
         download_figure(method, analysis_result, format="svg")
 
     with c3:
-        download_preprocessing_info(
-            method, analysis_result
-        )  # TODO this should go elsewhere
+        download_analysis_and_preprocessing_info(method, analysis_result, parameters)
+
+
+def display_df(df):
+    mask = df.applymap(type) != bool  # noqa: E721
+    d = {True: "TRUE", False: "FALSE"}
+    df = df.where(mask, df.replace(d))
+    st.dataframe(df)
 
 
 def download_figure(method, plot, format):
@@ -70,22 +66,35 @@ def download_figure(method, plot, format):
     st.download_button(label="Download as " + format, data=buffer, file_name=filename)
 
 
-def download_preprocessing_info(method, plot):
-    preprocesing_dict = plot.preprocessing
-    df = pd.DataFrame(preprocesing_dict.items())
-    filename = "plot" + method + "preprocessing_info.csv"
+def download_analysis_and_preprocessing_info(method, plot, parameters):
+    parameters_pretty = {f"analysis_parameter__{k}": v for k, v in parameters.items()}
+    dict_to_save = {
+        **plot.preprocessing,
+        **parameters_pretty,
+    }  # TODO why is the preprocessing info saved in the plots?
+
+    df = pd.DataFrame(dict_to_save.items())
+
+    filename = "plot" + method + "analysis_info.csv"
     csv = convert_df(df)
     st.download_button(
-        "Download DataSet Info as .csv",
+        "Download Analysis info as .csv",
         csv,
         filename,
         "text/csv",
     )
 
 
+def save_plot_to_session_state(method, plot, parameters):
+    """
+    save plot with method to session state to retrieve old results
+    """
+    st.session_state[StateKeys.PLOT_LIST] += [(method, plot, parameters)]
+
+
 def gather_parameters_and_do_analysis(
     analysis_name: str,
-) -> Tuple[Optional[Any], Optional[Any], Dict[str, Any]]:
+) -> Tuple[Optional[Any], Optional[Any], Optional[Dict[str, Any]]]:
     """Extract plotting options and display.
 
     Returns a tuple(figure, analysis_object, parameters) where figure is the plot,