Optimized code logic for offline enrichment analysis, added backgroun…

…d parameter
Starlitnightly · Sep 21, 2024 · 3f6b539 · 3f6b539
1 parent b522c2a
commit 3f6b539
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Showing 5 changed files with 15 additions and 9 deletions.
diff --git a/omicverse/bulk/_Enrichment.py b/omicverse/bulk/_Enrichment.py
@@ -280,7 +280,7 @@ class pyGSE(object):
 
     def __init__(self,gene_list:list,pathways_dict:dict,pvalue_threshold:float=0.05,pvalue_type:str='auto',
                  background=None,organism:str='Human',description:str='None',outdir:str='./enrichr',cutoff:float=0.5) -> None:
-        """Initialize the pyGSEA class.
+        """Initialize the pyGSE class.
 
         Arguments:
             gene_list: A list of genes.

diff --git a/omicverse/pl/_single.py b/omicverse/pl/_single.py
@@ -38,14 +38,10 @@
 from scanpy.plotting import _utils 
 
 from scanpy.plotting._utils import (
-    _IGraphLayout,
     _FontWeight,
     _FontSize,
     ColorLike,
     VBound,
-    circles,
-    check_projection,
-    check_colornorm,
 )
 
 def embedding(

diff --git a/omicverse/utils/_scatterplot.py b/omicverse/utils/_scatterplot.py
@@ -32,7 +32,6 @@
 from scanpy.plotting import _utils 
 
 from scanpy.plotting._utils import (
-    _IGraphLayout,
     _FontWeight,
     _FontSize,
     ColorLike,
@@ -813,7 +812,7 @@ def diffmap(adata, **kwargs) -> Union[Axes, List[Axes], None]:
     show_save_ax=doc_show_save_ax,
 )
 def draw_graph(
-    adata: AnnData, *, layout: Optional[_IGraphLayout] = None, **kwargs
+    adata: AnnData, *, layout = None, **kwargs
 ) -> Union[Axes, List[Axes], None]:
     """\
     Scatter plot in graph-drawing basis.

diff --git a/omicverse_guide/docs/Release_notes.md b/omicverse_guide/docs/Release_notes.md
@@ -471,4 +471,5 @@ Support Raw Windows platform
 
 ### Bulk Module
 
-- Fixed the import error of `gseapy` in `bulk.geneset_enrichment`
+- Fixed the import error of `gseapy` in `bulk.geneset_enrichment`
+- Optimized code logic for offline enrichment analysis, added background parameter
diff --git a/omicverse_guide/docs/Tutorials-bulk/t_deg.ipynb b/omicverse_guide/docs/Tutorials-bulk/t_deg.ipynb
@@ -924,7 +924,17 @@
    "id": "477e6940-4e9a-4df3-852b-ee354e57cf9b",
    "metadata": {},
    "source": [
-    "Note that the `pvalue_type` we set to `auto`, this is because when the genesets we enrichment if too small, use the `adjusted pvalue` we can't get the correct result. So you can set `adjust` or `raw` to get the significant geneset."
+    "Note that the `pvalue_type` we set to `auto`, this is because when the genesets we enrichment if too small, use the `adjusted pvalue` we can't get the correct result. So you can set `adjust` or `raw` to get the significant geneset.\n",
+    "\n",
+    "If you didn't have internet, please set `background` to all genes expressed in rna-seq,like:\n",
+    "\n",
+    "```python\n",
+    "enr=ov.bulk.geneset_enrichment(gene_list=deg_genes,\n",
+    "                                pathways_dict=pathway_dict,\n",
+    "                                pvalue_type='auto',\n",
+    "                                background=dds.result.index.tolist(),\n",
+    "                                organism='mouse')\n",
+    "```"
    ]
   },
   {