Scanpy: .var

AnnData.var

store the metadata of genes (features)

Data type:

>>> type(scanpy_object_used.var)
anndata._core.views.DataFrameView

Note: .var 的格式是 DataFrameView 而不是 DataFrame，采用以下方式进行 转换

kk=pd.DataFrame(scanpy_object_used.var)     '# 将 DataFrameView 转换为 DataFrame
type(kk)
kk.iloc[:3, :3]     #查看 前3行 和 前3列 的信息

Shape:

>>> scanpy_object_used.var.shape
(13714, 7)

AnnData.var.highly_variable

the highly variable gene names

>>> type(scanpy_object.var.highly_variable)
type(scanpy_object.var.highly_variable)

>>> scanpy_object.var.highly_variable[3:8]     # view the 3:8 top variable genes

---

AnnData.obs_names

the name of cells (barcodes)

Data type:

>>> type(scanpy_object_used.obs_names)
pandas.core.indexes.base.Index

Length:

>>> len(scanpy_object_used.obs_names)
2643     '# 细胞数量为 2643

取值:

>>> scanpy_object_used.obs_names[:3]
Index(['AAACATACAACCAC-1', 'AAACATTGAGCTAC-1', 'AAACATTGATCAGC-1'], dtype='object')

---

AnnData.var_names

the name of genes (features)

Data type:

>>> type(scanpy_object_used.var_names)
pandas.core.indexes.base.Index

Length:

>>> len(scanpy_object_used.var_names)
13714     '# 基因数量为 13714

取值:

>>> scanpy_object_used.var_names[5:9]
Index(['NOC2L', 'KLHL17', 'PLEKHN1', 'RP11-54O7.17'], dtype='object')