1.0.6

gseapy/__init__.py

@@ -8,16 +8,9 @@
 from .biomart import Biomart
 from .enrichr import Enrichr
 from .gsea import GSEA, Prerank, Replot, SingleSampleGSEA
+from .msigdb import Msigdb
 from .parser import get_library, get_library_name, read_gmt
-from .plot import (
-    barplot,
-    dotplot,
-    enrichment_map,
-    gseaplot,
-    gseaplot2,
-    heatmap,
-    ringplot,
-)
+from .plot import barplot, dotplot, enrichment_map, gseaplot, gseaplot2, heatmap
 
 
 def gsea(
@@ -640,7 +633,6 @@ def enrich(
     "dotplot",
     "barplot",
     "enrichment_map",
-    "ringplot",
     "heatmap",
     "gseaplot",
     "gseaplot2",
@@ -656,6 +648,7 @@ def enrich(
     "SingleSampleGSEA",
     "Enrichr",
     "Biomart",
+    "Msigdb",
     "get_library",
     "get_library_name",
     "read_gmt",

gseapy/msigdb.py

@@ -10,9 +10,9 @@ def __init__(self, dbver: str = "2023.1.Hs"):
         dbver: MSIGDB version number. default: 2023.1.Hs
         """
         self.url = "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/"
+        self._pattern = re.compile("(\w.+)\.(v\d.+)\.(entrez|symbols)\.gmt")
         self._db_version = self._get_db_version()
         self.categoires = self.list_category(dbver)
-        self._pattern = re.compile("(\w.+)\.(v\d.+)\.(entrez|symbols)\.gmt")
 
     def _get_db_version(self):
         resp = requests.get(self.url)
@@ -28,7 +28,10 @@ def get_gmt(
         self, category: str = "h.all", dbver: str = "2023.1.Hs", entrez: bool = False
     ):
         """
-        example: "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.1.Hs/c2.cp.kegg.v2023.1.Hs.entrez.gmt"
+        :params category: choose one from .list_category()
+        :params dbver: choose one from .list_dbver()
+
+        An example of query url: "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.1.Hs/c2.cp.kegg.v2023.1.Hs.entrez.gmt"
         """
         identifier = "symbols"
         if entrez:
@@ -47,9 +50,10 @@ def list_dbver(self):
         # self._db_version.columns = ["dbver", "date"]
         return self._db_version
 
-    def list_category(self, dbver):
+    def list_category(self, dbver: str = "2023.1.Hs"):
         """
         dbver: MSIGDB version number. default: 2023.1.Hs
+        see a list of dbver, call .list_dbver()
         """
         d = self.list_gmt(dbver)
         if d is not None:
@@ -61,7 +65,7 @@ def list_category(self, dbver):
             return categories.to_list()
         return None
 
-    def list_gmt(self, db):
+    def list_gmt(self, db: str):
         url = self.url + db
         resp = requests.get(url)
         if resp.ok: