Merge pull request #352 from MannLabs/simplify_analysis-III

simplify_analysis-III

alphastats/gui/pages/04_Analysis.py

@@ -1,35 +1,18 @@
 import streamlit as st
-from gui.utils.options import get_plotting_options, get_statistic_options
 
 from alphastats.gui.utils.analysis_helper import (
     display_df,
-    display_figure,
-    download_figure,
-    download_preprocessing_info,
-    get_analysis,
-    save_plot_to_session_state,
+    display_plot,
+    do_analysis,
 )
+from alphastats.gui.utils.options import get_plotting_options, get_statistic_options
 from alphastats.gui.utils.ui_helper import (
     StateKeys,
     convert_df,
     init_session_state,
     sidebar_info,
 )
 
-
-def select_analysis():
-    """
-    select box
-    loads keys from option dicts
-    """
-    method = st.selectbox(
-        "Analysis",
-        options=list(get_plotting_options(st.session_state).keys())
-        + list(get_statistic_options(st.session_state).keys()),
-    )
-    return method
-
-
 init_session_state()
 sidebar_info()
 
@@ -50,90 +33,49 @@ def select_analysis():
 st.markdown(styl, unsafe_allow_html=True)
 
 
-if StateKeys.PLOT_LIST not in st.session_state:
-    st.session_state[StateKeys.PLOT_LIST] = []
-
-
-if StateKeys.DATASET in st.session_state:
-    c1, c2 = st.columns((1, 2))
-
-    plot_to_display = False
-    df_to_display = False
-    method_plot = None
-
-    with c1:
-        method = select_analysis()
-
-        if method in (plotting_options := get_plotting_options(st.session_state)):
-            analysis_result = get_analysis(method=method, options_dict=plotting_options)
-            plot_to_display = True
-
-        elif method in (statistic_options := get_statistic_options(st.session_state)):
-            analysis_result = get_analysis(
-                method=method,
-                options_dict=statistic_options,
-            )
-            df_to_display = True
-
-        st.markdown("")
-        st.markdown("")
-        st.markdown("")
-        st.markdown("")
-
-    with c2:
-        # --- Plot -------------------------------------------------------
-
-        if analysis_result is not None and method != "Clustermap" and plot_to_display:
-            display_figure(analysis_result)
-
-            save_plot_to_session_state(analysis_result, method)
-
-            method_plot = [method, analysis_result]
-
-        elif method == "Clustermap":
-            st.write("Download Figure to see full size.")
-
-            display_figure(analysis_result)
-
-            save_plot_to_session_state(analysis_result, method)
-
-        # --- STATISTICAL ANALYSIS -------------------------------------------------------
-
-        elif analysis_result is not None and df_to_display:
-            display_df(analysis_result)
-
-            filename = method + ".csv"
-            csv = convert_df(analysis_result)
-
-    if analysis_result is not None and method != "Clustermap" and plot_to_display:
-        col1, col2, col3 = st.columns([1, 1, 1])
-
-        with col1:
-            download_figure(method_plot, format="pdf")
+if StateKeys.DATASET not in st.session_state:
+    st.info("Import Data first")
+    st.stop()
 
-        with col2:
-            download_figure(method_plot, format="svg")
+# --- SELECTION -------------------------------------------------------
+show_plot = False
+show_df = False
+analysis_result = None
 
-        with col3:
-            download_preprocessing_info(method_plot)
+c1, *_ = st.columns([1, 1, 1])
+with c1:
+    method = st.selectbox(
+        "Analysis",
+        options=["<select>"]
+        + ["------- plots -------"]
+        + list(get_plotting_options(st.session_state).keys())
+        + ["------- statistics -------"]
+        + list(get_statistic_options(st.session_state).keys()),
+    )
 
-    elif analysis_result is not None and df_to_display and method_plot:
-        col1, col2, col3 = st.columns([1, 1, 1])
+    if method in (plotting_options := get_plotting_options(st.session_state)):
+        analysis_result = do_analysis(method, options_dict=plotting_options)
+        show_plot = analysis_result is not None
 
-        with col1:
-            download_figure(method_plot, format="pdf", plotting_library="seaborn")
+    elif method in (statistic_options := get_statistic_options(st.session_state)):
+        analysis_result = do_analysis(
+            method,
+            options_dict=statistic_options,
+        )
+        show_df = analysis_result is not None
 
-        with col2:
-            download_figure(method_plot, format="svg", plotting_library="seaborn")
 
-        with col3:
-            download_preprocessing_info(method_plot)
+# --- SHOW PLOT -------------------------------------------------------
+if show_plot:
+    display_plot(method, analysis_result)
 
-    elif analysis_result is not None and df_to_display:
-        st.download_button(
-            "Download as .csv", csv, filename, "text/csv", key="download-csv"
-        )
+# --- SHOW STATISTICAL ANALYSIS -------------------------------------------------------
+elif show_df:
+    display_df(analysis_result)
 
+    csv = convert_df(analysis_result)
 
-else:
-    st.info("Import Data first")
+    # TODO do we want to save statistical analysis to results page as well?
+    st.download_button(
+        "Download as .csv", csv, method + ".csv", "text/csv", key="download-csv"
+    )

alphastats/gui/pages/05_LLM.py

@@ -197,7 +197,7 @@ def select_analysis():
         st.stop()
     print("genes_of_interest", genes_of_interest_colored)
 
-    save_plot_to_session_state(volcano_plot, method)
+    save_plot_to_session_state(method, volcano_plot)
     st.session_state[StateKeys.GENES_OF_INTEREST_COLORED] = genes_of_interest_colored
     # st.session_state["gene_functions"] = get_info(genes_of_interest_colored, organism)
     st.session_state[StateKeys.UPREGULATED] = [

alphastats/gui/pages/06_Results.py

@@ -1,74 +1,32 @@
-import io
-
-import pandas as pd
 import streamlit as st
 
+from alphastats.gui.utils.analysis_helper import display_plot
 from alphastats.gui.utils.ui_helper import (
     StateKeys,
-    convert_df,
     init_session_state,
     sidebar_info,
 )
 
-
-def display_plotly_figure(plot):
-    st.plotly_chart(plot)
-
-
-def save_plotly(plot, name, format):
-    # Create an in-memory buffer
-    buffer = io.BytesIO()
-    # Save the figure as a pdf to the buffer
-    plot.write_image(file=buffer, format=format)
-    st.download_button(
-        label="Download as " + format, data=buffer, file_name=name + "." + format
-    )
-
-
-def download_preprocessing_info(plot, name, count):
-    preprocesing_dict = plot.preprocessing
-    df = pd.DataFrame(preprocesing_dict.items())
-    filename = "plot" + name + "preprocessing_info.csv"
-    csv = convert_df(df)
-    print("preprocessing" + count)
-    st.download_button(
-        "Download DataSet Info as .csv",
-        csv,
-        filename,
-        "text/csv",
-        key="preprocessing" + count,
-    )
-
-
 init_session_state()
 sidebar_info()
 
 st.markdown("### Results")
 
+if not st.session_state[StateKeys.PLOT_LIST]:
+    st.info("No analysis saved yet.")
+    st.stop()
 
-if StateKeys.PLOT_LIST in st.session_state:
-    for count, plot in enumerate(st.session_state[StateKeys.PLOT_LIST]):
-        print("plot", type(plot), count)
-        count = str(count)
-
-        st.markdown("\n\n")
-        name = plot[0]
-        plot = plot[1]
-        if name == "ttest":
-            plot = plot.plot
-        st.write(name)
-
-        display_plotly_figure(plot)
+for count, saved_item in enumerate(st.session_state[StateKeys.PLOT_LIST]):
+    print("plot", type(saved_item), count)
 
-        col1, col2, col3 = st.columns([1, 1, 1])
+    method = saved_item[0]
+    plot = saved_item[1]
 
-        with col1:
-            save_plotly(plot, name + count, format="pdf")
+    st.markdown("\n\n\n")
+    st.markdown(f"#### {method}")
 
-        with col2:
-            save_plotly(plot, name + count, format="svg")
+    if st.button("x remove analysis", key="remove" + method + str(count)):
+        st.session_state[StateKeys.PLOT_LIST].remove(saved_item)
+        st.rerun()
 
-        with col3:
-            download_preprocessing_info(plot, name, count)
-else:
-    st.info("No analysis performed yet.")
+    display_plot(method + str(count), plot, show_save_button=False)