Fixed the error of log_init in gsea_obj.enrichment (#184)

omicverse/externel/gseapy/gsea.py

@@ -349,7 +349,8 @@ def __init__(self, data, gene_sets, classes, outdir='GSEA_output',
         self._noplot=no_plot
         # init logger
         logfile = self.prepare_outdir()
-        self._logger = log_init(outlog=logfile,
+        self._logger = log_init(name='gseapy',
+                                filename=logfile,
                                 log_level=logging.INFO if self.verbose else logging.WARNING)
 
     def load_data(self, cls_vec):
@@ -481,7 +482,8 @@ def __init__(self, rnk, gene_sets, outdir='GSEA_prerank',
         self._noplot=no_plot
         # init logger
         logfile = self.prepare_outdir()
-        self._logger = log_init(outlog=logfile,
+        self._logger = log_init(name='gseapy',
+                                filename=logfile,
                                 log_level=logging.INFO if self.verbose else logging.WARNING)
 
 
@@ -558,7 +560,8 @@ def __init__(self, data, gene_sets, outdir="GSEA_SingleSample", sample_norm_meth
         # init logger
 
         logfile = self.prepare_outdir()
-        self._logger = log_init(outlog=logfile,
+        self._logger = log_init(name='gseapy',
+                                filename=logfile,
                                 log_level=logging.INFO if self.verbose else logging.WARNING)
 
     def corplot(self):
@@ -814,7 +817,8 @@ def __init__(self, indir, outdir='GSEApy_Replot', weighted_score_type=1,
         # init logger
         mkdirs(self.outdir)
         outlog = os.path.join(self.outdir,"gseapy.%s.%s.log"%(self.module,"run"))
-        self._logger = log_init(outlog=outlog,
+        self._logger = log_init(name='gseapy',
+                                filename=logfile,
                                 log_level=logging.INFO if self.verbose else logging.WARNING)
     def run(self):
         """main replot function"""

omicverse/single/_SCSA.py

@@ -1122,6 +1122,7 @@ def get_cell_matrix_detail(self,exps,ltitle,fid,gcol,ccol,usertag,abs_tag):
         #print(rownames)
         #print(colnames)
         #print(cell_matrix)
+
 
         if self.noprint == False:
             if usertag:

omicverse/space/_cast.py

@@ -0,0 +1,34 @@
+from scipy.sparse import csr_matrix,issparse
+import numpy as np
+import os
+from tqdm import tqdm
+import pandas as pd
+
+def CAST(adata,sample_key=None,basis='spatial',layer='norm_1e4',
+        output_path = 'output/CAST_Mark',gpu_t=0,device='cuda:0',**kwargs):
+    if issparse(adata.obsm[basis]):
+        adata.obsm[basis]=adata.obsm[basis].toarray()
+    adata.obs['x'] = adata.obsm[basis][:,0]
+    adata.obs['y'] = adata.obsm[basis][:,1]
+
+
+    # Get the coordinates and expression data for each sample
+    samples = np.unique(adata.obs[sample_key]) # used samples in adata
+    coords_raw = {sample_t: np.array(adata.obs[['x','y']])[adata.obs[sample_key] == sample_t] for sample_t in samples}
+    exp_dict = {sample_t: adata[adata.obs[sample_key] == sample_t].layers['norm_1e4'] for sample_t in samples}
+
+
+    os.makedirs(output_path, exist_ok=True)
+
+    from ..externel.CAST import CAST_MARK
+    embed_dict = CAST_MARK(coords_raw,exp_dict,output_path,gpu_t=gpu_t,device=device,**kwargs)
+
+
+    adata.obsm['X_cast']=np.zeros((adata.shape[0],512))
+
+    adata.obsm['X_cast']=pd.DataFrame(adata.obsm['X_cast'],index=adata.obs.index)
+    for key in tqdm(embed_dict.keys()):
+        adata.obsm['X_cast'].loc[adata.obs[sample_key]==key]+=embed_dict[key].cpu().numpy()
+    adata.obsm['X_cast']=adata.obsm['X_cast'].values
+    print('CAST embedding is saved in adata.obsm[\'X_cast\']')
+    #adata.obs['cast_clusters']=adata.obs['cast_clusters'].astype('category')

omicverse_guide/docs/Release_notes.md

@@ -485,4 +485,10 @@ Support Raw Windows platform
 ### PP Module
 
 - Fixed a return bugs in `pp.regress_and_scale` (#156)
-- Fixed a scanpy version error when using `ov.pp.pca` (#154)
+- Fixed a scanpy version error when using `ov.pp.pca` (#154)
+
+## v 1.6.8
+
+### Bulk Module
+
+- Fixed the error of log_init in gsea_obj.enrichment (#184)