annotate/popv

Description

Performs popular major vote cell typing on single cell sequence data using multiple algorithms. Note that this is a one-shot version of PopV.

Type

python_script

Launch

Inputs

Name	Type & Properties	Description
--input -i	file required	Input h5mu file.
--modality	string	Which modality to process.
--input_layer	string	Which layer to use. If no value is provided, the counts are assumed to be in the `.X` slot. Otherwise, count data is expected to be in `.layers[input_layer]`.
--input_obs_batch	string	Key in obs field of input adata for batch information. If no value is provided, batch label is assumed to be unknown.
--input_var_subset	string	Subset the input object with this column.
--input_obs_label	string	Key in obs field of input adata for label information. This is only used for training scANVI. Unlabelled cells should be set to `"unknown_celltype_label"`.
--unknown_celltype_label	string	If `input_obs_label` is specified, cells with this value will be treated as unknown and will be predicted by the model.

Name

Type & Properties

--input

-i

file

required

--modality

string

--input_layer

string

--input_obs_batch

string

--input_var_subset

string

--input_obs_label

string

--unknown_celltype_label

string

Reference

Name	Type & Properties	Description
--reference	file required	User-provided reference tissue. The data that will be used as reference to call cell types.
--reference_layer	string	Which layer to use. If no value is provided, the counts are assumed to be in the `.X` slot. Otherwise, count data is expected to be in `.layers[reference_layer]`.
--reference_obs_label	string	Key in obs field of reference AnnData with cell-type information.
--reference_obs_batch	string	Key in obs field of input adata for batch information.

Name

Type & Properties

--reference

file

required

--reference_layer

string

--reference_obs_label

string

--reference_obs_batch

string

Outputs

Name	Type & Properties	Description
--output	file required output	Output h5mu file.
--output_compression	string

Name

Type & Properties

--output

file

required

output

--output_compression

string

Arguments

Name	Type & Properties	Description
--methods	string required multiple	Methods to call cell types. By default, runs to knn_on_scvi and scanvi.

Name

Type & Properties

--methods

string

required

multiple