labels_transfer/knn

Description

Performs label transfer from reference to query using KNN classifier

Type

python_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
reference_obsm_features: [ "X_integrated_scanvi" ]  
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"  
output_uns_parameters: [ "labels_transfer" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.3 \  
  -main-script target/nextflow/labels_transfer/knn/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 required	The `.obsm` key of the embedding to use for the classifier's training. 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 of the target labels to tranfer.

Name

Type & Properties

--reference

file

--reference_obsm_features

string

required

--reference_obs_targets

string

multiple

Outputs

Name	Type & Properties	Description
--output	file required output	The query data in .h5mu format with predicted labels transfered 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_uncertainty	string multiple	In which `.obs` slots to store the uncertainty 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 `"_uncertainty"` suffix.
--output_uns_parameters	string	The `.uns` key to store additional information about the parameters used for the label transfer.

Name

Type & Properties

--output

file

required

output

--output_obs_predictions

string

multiple

--output_obs_uncertainty

string

multiple

--output_uns_parameters

string

Learning parameters

Name	Type & Properties	Description
--n_neighbors -k	integer required	Number of nearest neighbors to use for classification

Name

Type & Properties

--n_neighbors

-k

integer

required