daklab
diff --git a/‎LeafletSC.egg-info/PKG-INFO‎
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diff --git a/‎LeafletSC/clustering/find_intron_clusters.py‎
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diff --git a/‎Tutorials/01_run_intron_clustering.ipynb‎
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diff --git a/‎build/lib/LeafletSC/clustering/find_intron_clusters.py‎
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diff --git a/‎data/processed/test_intron_clusters_50_500000_2_20240314_single_cell.gz‎
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diff --git a/‎data/processed/test_intron_clusters_50_500000_2_20240319_single_cell.gz‎
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diff --git a/‎data/processed/test_intron_clusters_50_500000_2_20240423_single_cell.gz‎
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diff --git a/‎data/processed/test_juncs.bed‎
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diff --git a/‎dist/LeafletSC-0.2.19.tar.gz‎
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diff --git a/‎dist/LeafletSC-0.2.19-py3-none-any.whl‎ ‎dist/LeafletSC-0.2.2-py3-none-any.whl‎dist/LeafletSC-0.2.19-py3-none-any.whl renamed to dist/LeafletSC-0.2.2-py3-none-any.whl
30 KB b/‎dist/LeafletSC-0.2.19-py3-none-any.whl‎ ‎dist/LeafletSC-0.2.2-py3-none-any.whl‎dist/LeafletSC-0.2.19-py3-none-any.whl renamed to dist/LeafletSC-0.2.2-py3-none-any.whl
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@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: LeafletSC
-Version: 0.2.19
+Version: 0.2.2
 Summary: Alternative splicing quantification in single cells with Leaflet
 Home-page: https://github.com/daklab/Leaflet
 Author: Karin Isaev, Columbia University and NYGC
 
@@ -194,10 +194,13 @@ def read_junction_files(junc_files, junc_suffix):
         junc_path = Path(junc_path)
         print(f"Reading in junction files from {junc_path}")
 
-        junc_files_in_path = list(junc_path.rglob(junc_suffix))
-        if not junc_files_in_path:
-            print(f"No junction files found in {junc_path} with suffix {junc_suffix}")
-            continue
+        if junc_path.is_dir():
+            junc_files_in_path = list(junc_path.rglob(junc_suffix))
+            if not junc_files_in_path:
+                print(f"No junction files found in {junc_path} with suffix {junc_suffix}")
+                continue
+        else:
+            junc_files_in_path = [junc_path]
 
         print(f"The number of junction files to be processed is {len(junc_files_in_path)}")
 
@@ -400,7 +403,11 @@ def main(junc_files, gtf_file, output_file, sequencing_type, junc_bed_file, thre
     #1. Check format of junc_files and convert to list if necessary
     # Can either be a list of folders with junction files or a single folder with junction files
 
-    if "," in junc_files:
+    # first check if junc_files is a list already 
+    if type(junc_files) == list:
+        # do nothing 
+        pass
+    elif "," in junc_files:
         junc_files = junc_files.split(",")
     else:
         # if junc_files is a single file, then convert it to a list
 
@@ -210,7 +210,7 @@ def read_junction_files(junc_files, junc_suffix):
                 juncs['cell_type'] = junc_file
                 all_juncs_list.append(juncs)  # Append the DataFrame to the list
             except Exception as e:
-                print(f"Could not read in {junc_file}: {e}")
+                #print(f"Could not read in {junc_file}: {e}")
                 files_not_read.append(junc_file)
 
     if len(files_not_read) > 0:
@@ -305,10 +305,13 @@ def mapping_juncs_exons(juncs_gr, gtf_exons_gr, singletons):
 def basepair_to_kilobase(bp):
     return bp / 1000  # Convert base pairs to kilobases
 
-def visualize_junctions(dat, junc_id, p_usage_ratio=True):
+def visualize_local_events(dat, junc_id=None, cluster_id=None, p_usage_ratio=True):
 
-    # Filter data for the specific junction ID
-    dat = dat[dat.Cluster == dat[dat.junction_id == junc_id].Cluster.values[0]]
+    # Filter dat based on junc_id, or cluster_id 
+    if junc_id is not None:
+        dat = dat[dat.Cluster == dat[dat.junction_id == junc_id].Cluster.values[0]]
+    elif cluster_id is not None:
+        dat = dat[dat.Cluster == cluster_id]
 
     # Get junctions
     juncs = dat[["chrom", "chromStart", "chromEnd", "strand", "intron_length", "counts_total", "Start_b", "End_b", "exon_id"]]