labels_transfer/cellmapper

Description

Transfer labels from a reference to a query using CellMapper in a shared
embedding space.

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
reference_obs_targets:  
  [  
    "ann_level_1",  
    "ann_level_2",  
    "ann_level_3",  
    "ann_level_4",  
    "ann_level_5",  
    "ann_finest_level"  
  ]  
output: "$id.$key.output"  
n_neighbors: [ 15 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/labels_transfer/cellmapper/main.nf \  
  -params-file params.yaml

Input dataset (query) arguments

Name	Type & Properties	Description
--input	file required	The query data to transfer the labels to. Should be a .h5mu file.
--modality	string	Which modality to use.
--input_obsm_features	string	The `.obsm` key of the embedding to use for the classifier's inference. If not provided, the `.X` slot will be used instead. Make sure that embedding was obtained in the same way as the reference embedding (e.g. by the same model or preprocessing).

Name

Type & Properties

--input

file

required

--modality

string

--input_obsm_features

string

Reference dataset arguments

Name	Type & Properties	Description
--reference	file	The reference data to train classifiers on.
--reference_obsm_features	string	The `.obsm` key of the embedding to use for the classifier's training. If not provided, the `.X` slot will be used instead. Make sure that embedding was obtained in the same way as the query embedding (e.g. by the same model or preprocessing).
--reference_obs_targets	string multiple	The `.obs` key(s) of the target labels to transfer.

Name

Type & Properties

--reference

file

--reference_obsm_features

string

--reference_obs_targets

string

multiple

Outputs

Name	Type & Properties	Description
--output	file required output	The query data in .h5mu format with predicted labels transferred from the reference.
--output_obs_predictions	string multiple	In which `.obs` slots to store the predicted information. If provided, must have the same length as `--reference_obs_targets`. If empty, will default to the `reference_obs_targets` combined with the `"_pred"` suffix.
--output_obs_probability	string multiple	In which `.obs` slots to store the probability of the predictions. If provided, must have the same length as `--reference_obs_targets`. If empty, will default to the `reference_obs_targets` combined with the `"_probability"` suffix.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata H5 files. By default no compression is applied.

Name

Type & Properties

--output

file

required

output

--output_obs_predictions

string

multiple

--output_obs_probability

string

multiple

--output_compression

string

CellMapper arguments

Name	Type & Properties	Description
--n_neighbors	integer	Number of neighbors used by CellMapper.
--kernel_method	string	Method to use for computing the CellMapper mapping matrix.

Name

Type & Properties

--n_neighbors

integer

--kernel_method

string