neighbors/bbknn

Description

BBKNN network generation

Type

python_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
obsm_input: [ "X_pca" ]  
obs_batch: [ "batch" ]  
output: "$id.$key.output.h5mu"  
uns_output: [ "neighbors" ]  
obsp_distances: [ "distances" ]  
obsp_connectivities: [ "connectivities" ]  
n_neighbors_within_batch: [ 3 ]  
n_pcs: [ 50 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.3 \  
  -main-script target/nextflow/neighbors/bbknn/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--modality	string
--obsm_input	string	The dimensionality reduction in `.obsm` to use for neighbour detection. Defaults to X_pca.
--obs_batch	string	.obs column name discriminating between your batches.
--output -o	file required output	Output .h5mu file.
--output_compression	string	The compression format to be used on the output h5mu object.
--uns_output	string	Mandatory .uns slot to store various neighbor output objects.
--obsp_distances	string	In which .obsp slot to store the distance matrix between the resulting neighbors.
--obsp_connectivities	string	In which .obsp slot to store the connectivities matrix between the resulting neighbors.
--n_neighbors_within_batch	integer	How many top neighbours to report for each batch; total number of neighbours in the initial k-nearest-neighbours computation will be this number times the number of batches.
--n_pcs	integer	How many dimensions (in case of PCA, principal components) to use in the analysis.
--n_trim	integer	Trim the neighbours of each cell to these many top connectivities. May help with population independence and improve the tidiness of clustering. The lower the value the more independent the individual populations, at the cost of more conserved batch effect. If `None` (default), sets the parameter value automatically to 10 times `neighbors_within_batch` times the number of batches. Set to 0 to skip.

Name

Type & Properties

--input

-i

file

required

--modality

string

--obsm_input

string

--obs_batch

string

--output

-o

file

required

output

--output_compression

string

--uns_output

string

--obsp_distances

string

--obsp_connectivities

string

--n_neighbors_within_batch

integer

--n_pcs

integer

--n_trim

integer