add logfoldchanges, #1

genecell · Aug 10, 2021 · b6df4c0 · b6df4c0
1 parent 0374729
commit b6df4c0
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diff --git a/build/lib/cosg/cosg.py b/build/lib/cosg/cosg.py
@@ -6,10 +6,7 @@
 from typing import Iterable, Union, Optional
 
 
-<<<<<<< HEAD
 
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
 ### Refer to: https://github.com/theislab/scanpy/blob/5533b644e796379fd146bf8e659fd49f92f718cd/scanpy/_compat.py
 try:
     from typing import Literal
@@ -27,17 +24,13 @@ def __getitem__(cls, values):
         class Literal(metaclass=LiteralMeta):
             pass
 
-<<<<<<< HEAD
 ### Refer to Scanpy       
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
 def _select_top_n(scores, n_top):
     reference_indices = np.arange(scores.shape[0], dtype=int)
     partition = np.argpartition(scores, -n_top)[-n_top:]
     partial_indices = np.argsort(scores[partition])[::-1]
     global_indices = reference_indices[partition][partial_indices]
     return global_indices
-<<<<<<< HEAD
 
 
 ### Import from Scanpy
@@ -315,8 +308,6 @@ def _basic_stats(self):
                 # deleting the next line causes a memory leak for some reason
                 del X_rest
 
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
 
 def cosg(
     adata,
@@ -329,10 +320,7 @@ def cosg(
 
     n_genes_user:int =50,
     key_added: Optional[str] = None,
-<<<<<<< HEAD
     calculate_logfoldchanges: bool = True,
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
     use_raw: bool = True,
     layer: Optional[str] = None,
     reference: str = 'rest',    
@@ -361,11 +349,8 @@ def cosg(
         The number of genes that appear in the returned tables. The default value is 50.
     key_added
         The key in `adata.uns` information is saved to.
-<<<<<<< HEAD
     calculate_logfoldchanges
         Calculate logfoldchanges.
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
     use_raw
         Use `raw` attribute of `adata` if present.
     layer
@@ -496,7 +481,6 @@ def cosg(
     ### Refer to scanpy
     rank_stats=None
 
-<<<<<<< HEAD
     ### Whether to calculate logfoldchanges, because this is required in scanpy 1.8
     if calculate_logfoldchanges:
         ### Calculate basic stats
@@ -521,8 +505,6 @@ def cosg(
         anndata_obj = _RankGenes(adata, groups_order2, groupby, reference, use_raw, layer, pts)
         anndata_obj._basic_stats()
 
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
 
     ### Refer to Scanpy
     # for correct getnnz calculation
@@ -561,7 +543,6 @@ def cosg(
             rank_stats = pd.DataFrame(columns=idx)
         rank_stats[group_i, 'names'] = adata.var_names[global_indices]
         rank_stats[group_i, 'scores'] = scores[global_indices]
-<<<<<<< HEAD
 
         if calculate_logfoldchanges:
             group_index=np.where(anndata_obj.groups_order==group_i)[0][0]
@@ -592,28 +573,15 @@ def cosg(
         'names': 'O',
         'scores': 'float32',
         }
-=======
-
-        order_i=order_i+1
-
-    ## Refer to scanpy
-    dtypes = {
-    'names': 'O',
-    'scores': 'float32',
-    }
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
     ###
     rank_stats.columns = rank_stats.columns.swaplevel()
     for col in rank_stats.columns.levels[0]:
         adata.uns[key_added][col]=rank_stats[col].to_records(
     index=False, column_dtypes=dtypes[col]
     )
 
-<<<<<<< HEAD
 
 
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
     print('**finished identifying marker genes by COSG**')
 
     ### Return the result

diff --git a/cosg.egg-info/PKG-INFO b/cosg.egg-info/PKG-INFO
@@ -7,7 +7,6 @@ Author: Min Dai
 Author-email: [email protected]
 License: BSD 3-Clause License
 Download-URL: https://github.com/genecell/COSG
-<<<<<<< HEAD
 Description: |Stars| |PyPI| |Docs| 
 
         .. |Stars| image:: https://img.shields.io/github/stars/genecell/COSG?logo=GitHub&color=yellow
@@ -18,9 +17,6 @@ Description: |Stars| |PyPI| |Docs|
            :target: https://cosg.readthedocs.io
 
         Accurate and fast cell marker gene identification with COSG
-=======
-Description: Accurate and fast cell marker gene identification with COSG
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
         =======================================================================================================
 
         Overview

diff --git a/cosg/cosg.py b/cosg/cosg.py
@@ -6,10 +6,7 @@
 from typing import Iterable, Union, Optional
 
 
-<<<<<<< HEAD
 
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
 ### Refer to: https://github.com/theislab/scanpy/blob/5533b644e796379fd146bf8e659fd49f92f718cd/scanpy/_compat.py
 try:
     from typing import Literal
@@ -27,17 +24,13 @@ def __getitem__(cls, values):
         class Literal(metaclass=LiteralMeta):
             pass
 
-<<<<<<< HEAD
 ### Refer to Scanpy       
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
 def _select_top_n(scores, n_top):
     reference_indices = np.arange(scores.shape[0], dtype=int)
     partition = np.argpartition(scores, -n_top)[-n_top:]
     partial_indices = np.argsort(scores[partition])[::-1]
     global_indices = reference_indices[partition][partial_indices]
     return global_indices
-<<<<<<< HEAD
 
 
 ### Import from Scanpy
@@ -315,8 +308,6 @@ def _basic_stats(self):
                 # deleting the next line causes a memory leak for some reason
                 del X_rest
 
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
 
 def cosg(
     adata,
@@ -329,10 +320,7 @@ def cosg(
 
     n_genes_user:int =50,
     key_added: Optional[str] = None,
-<<<<<<< HEAD
     calculate_logfoldchanges: bool = True,
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
     use_raw: bool = True,
     layer: Optional[str] = None,
     reference: str = 'rest',    
@@ -361,11 +349,8 @@ def cosg(
         The number of genes that appear in the returned tables. The default value is 50.
     key_added
         The key in `adata.uns` information is saved to.
-<<<<<<< HEAD
     calculate_logfoldchanges
         Calculate logfoldchanges.
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
     use_raw
         Use `raw` attribute of `adata` if present.
     layer
@@ -496,7 +481,6 @@ def cosg(
     ### Refer to scanpy
     rank_stats=None
 
-<<<<<<< HEAD
     ### Whether to calculate logfoldchanges, because this is required in scanpy 1.8
     if calculate_logfoldchanges:
         ### Calculate basic stats
@@ -521,8 +505,6 @@ def cosg(
         anndata_obj = _RankGenes(adata, groups_order2, groupby, reference, use_raw, layer, pts)
         anndata_obj._basic_stats()
 
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
 
     ### Refer to Scanpy
     # for correct getnnz calculation
@@ -561,7 +543,6 @@ def cosg(
             rank_stats = pd.DataFrame(columns=idx)
         rank_stats[group_i, 'names'] = adata.var_names[global_indices]
         rank_stats[group_i, 'scores'] = scores[global_indices]
-<<<<<<< HEAD
 
         if calculate_logfoldchanges:
             group_index=np.where(anndata_obj.groups_order==group_i)[0][0]
@@ -592,28 +573,15 @@ def cosg(
         'names': 'O',
         'scores': 'float32',
         }
-=======
-
-        order_i=order_i+1
-
-    ## Refer to scanpy
-    dtypes = {
-    'names': 'O',
-    'scores': 'float32',
-    }
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
     ###
     rank_stats.columns = rank_stats.columns.swaplevel()
     for col in rank_stats.columns.levels[0]:
         adata.uns[key_added][col]=rank_stats[col].to_records(
     index=False, column_dtypes=dtypes[col]
     )
 
-<<<<<<< HEAD
 
 
-=======
->>>>>>> 55514a16bf1a93c065806f56b111f8a9905c7362
     print('**finished identifying marker genes by COSG**')
 
     ### Return the result

diff --git a/dist/cosg-0.0.9-py3-none-any.whl b/dist/cosg-0.0.9-py3-none-any.whl
diff --git a/dist/cosg-0.0.9.tar.gz b/dist/cosg-0.0.9.tar.gz