sccloud.set_group_attribute

sccloud.set_group_attribute(data, attribute_string)[source]

Set group attributes used in batch correction.

Batch correction assumes the differences in gene expression between channels are due to batch effects. However, in many cases, we know that channels can be partitioned into several groups and each group is biologically different from others. In this case, sccloud will only perform batch correction for channels within each group.

data: anndata.AnnData

Annotated data matrix with rows for cells and columns for genes.

attribute_string: str
Attributes used to construct groups:

  • If None, assume all channels are from one group.

  • attr, where attr is a keyword in data.obs.

So the groups are defined by this sample attribute.

``att1+att2+…+attrn``, where ``attr1`` to ``attrn`` are keywords in ``data.obs``. So the groups are defined by the Cartesian product of these *n attributes.

  • attr=value_11,...value_1n_1;value_21,...value_2n_2;...;value_m1,...,value_mn_m, where attr is a keyword in data.obs.

In this form, there will be (m+1) groups. A cell belongs to group i (i > 1) if and only if its sample attribute attr has a value among value_i1, … value_in_i. A cell belongs to group 0 if it does not belong to any other groups.

None

Update data.obs:

  • data.obs["Group"]: Group ID for each cell.

>>> scc.set_group_attribute(adata, attr_string = "Individual")

>>> scc.set_group_attribute(adata, attr_string = "Individual+assignment")

>>> scc.set_group_attribute(adata, attr_string = "Channel=1,3,5;2,4,6,8")
Return type

None