Added a bit more information in the output tables of InsertsDict class and streamlit app.

src/plotting_on_genome/inserts_dict.py

@@ -321,6 +321,7 @@ class InsertsDict(object):
                     x.strand,
                     len(x),
                     x.coverage,
+                    x.matched,
                 )
                 for x in self.get(
                     insert_type=insert_type, filter_threshold=filter_threshold
@@ -328,13 +329,14 @@ class InsertsDict(object):
             ],
             columns=(
                 "seq_id",
-                "NCBI_accession_number",
+                "hit_id",
                 "insert_idx",
                 "insert_start",
                 "insert_end",
                 "insert_strand",
                 "insert_length",
                 "insert_coverage",
+                "insert_matched",
             ),
         )
 

streamlit_app.py

@@ -14,9 +14,6 @@ import plotting_on_genome as pog
 if "stage" not in st.session_state:
     st.session_state.stage = 0
 
-if "insert_type" not in st.session_state:
-    st.session_state.insert_type = "both"
-
 if "workdir" not in st.session_state:
     st.session_state.workdir = None
 
@@ -112,10 +109,6 @@ def get_main_inputs():
     fwd_suf = st.text_input("Forward suffix:", "_F", key="fwd_suf")
     rev_suf = st.text_input("Reverse suffix:", "_R", key="rev_suf")
 
-    st.session_state.insert_type = st.selectbox(
-        "insert types:", ["both", "matched", "unmatched"]
-    )
-
     if args.workdir:
         st.session_state.workdir = st.text_input("workdir", "Output")
 
@@ -142,7 +135,7 @@ def convert_df(df, **kwargs):
 
 def show_results():
     inserts_all = st.session_state.pipeline
-    insert_type = st.session_state.insert_type
+    insert_type = st.selectbox("Insert type:", ["both", "matched", "unmatched"])
 
     filter_threshold = st.slider("Filter threshold:", 0.0, 1.0, 0.7)
 
@@ -155,32 +148,40 @@ def show_results():
     )
     params = dict(insert_type=insert_type, filter_threshold=filter_threshold)
 
-    df_inserts = inserts_all.to_dataframe(**params)
-    df_genes = inserts_all.genes_to_dataframe(**params, buffer=buffer)
+    if inserts_all is not None:
 
-    st.download_button(
-        label="Download all inserts as CSV",
-        data=df_inserts.pipe(convert_df, index=False),
-        file_name="inserts.csv",
-        mime="text/csv",
-        use_container_width=True,
-    )
+        df_inserts = inserts_all.to_dataframe(**params)
+        df_genes = inserts_all.genes_to_dataframe(**params, buffer=buffer)
 
-    st.download_button(
-        label="Download all genes as CSV",
-        data=df_genes.pipe(convert_df, index=False),
-        file_name="genes.csv",
-        mime="text/csv",
-        use_container_width=True,
-    )
+        counts = df_inserts.groupby("insert_matched").insert_matched.count().to_dict()
+        counts = {val: counts[val] if val in counts else 0 for val in (True, False)}
+        st.write(
+            f"Number of inserts:\n "
+            f"- matched: {counts[True]}\n "
+            f"- unmatched: {counts[False]}"
+        )
 
-    option = st.selectbox(
-        "plot type:",
-        ["plot inserts", "plot genome", "plot insert dists"],
-        None,
-    )
+        st.download_button(
+            label="Download all inserts as CSV",
+            data=df_inserts.pipe(convert_df, index=False),
+            file_name="inserts.csv",
+            mime="text/csv",
+            use_container_width=True,
+        )
 
-    if inserts_all is not None:
+        st.download_button(
+            label="Download all genes as CSV",
+            data=df_genes.pipe(convert_df, index=False),
+            file_name="genes.csv",
+            mime="text/csv",
+            use_container_width=True,
+        )
+
+        option = st.selectbox(
+            "plot type:",
+            ["plot inserts", "plot genome", "plot insert dists"],
+            None,
+        )
 
         if option == "plot inserts":
 
@@ -202,6 +203,11 @@ def show_results():
                 st.write(df_genes.query("seq_id == @seq_id"))
 
                 for insert in inserts:
+                    st.write(
+                        f"Insert {insert.idx}: "
+                        f"coverage = {insert.coverage:.2f}, "
+                        f"matched = {insert.matched}"
+                    )
                     fig, axs = plt.subplots(2, 1, figsize=(10, 6), height_ratios=[3, 5])
                     fig.suptitle(f"Insert {insert.idx}")
                     axs = insert.plot(
@@ -217,11 +223,11 @@ def show_results():
 
         elif option == "plot genome":
 
-            st.write(df_inserts)
-
             labels = st.toggle("Labels")
             insert_idxs = None if st.toggle("Plot inserts", True) else []
 
+            st.write(df_inserts)
+
             fig, ax = plt.subplots(figsize=(10, 10 * (1 + 2 * labels)))
             ax = inserts_all.plot(insert_idxs, show_labels=labels, ax=ax, **params)
             st.pyplot(fig, use_container_width=True)