cluster/leiden

Description

Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy framework] [Wolf18].
Leiden is an improved version of the [Louvain algorithm] [Blondel08].
It has been proposed for single-cell analysis by [Levine15] [Levine15].
This requires having ran neighbors/find_neighbors or neighbors/bbknn first.

[Blondel08]: Blondel et al. (2008), Fast unfolding of communities in large networks, J. Stat. Mech.
[Levine15]: Levine et al. (2015), Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis, Cell.
[Traag18]: Traag et al. (2018), From Louvain to Leiden: guaranteeing well-connected communities arXiv.
[Wolf18]: Wolf et al. (2018), Scanpy: large-scale single-cell gene expression data analysis, Genome Biology.

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" ]  
obsp_connectivities: [ "connectivities" ]  
output: "$id.$key.output.h5mu"  
obsm_name: [ "leiden" ]  
resolution: [ 1 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.1 \  
  -main-script target/nextflow/cluster/leiden/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input file.
--modality	string	Which modality from the input MuData file to process.
--obsp_connectivities	string	In which .obsp slot the neighbor connectivities can be found.
--output -o	file required output	Output file.
--obsm_name	string	Name of the .obsm key under which to add the cluster labels. The name of the columns in the matrix will correspond to the resolutions.
--resolution	double required multiple	A parameter value controlling the coarseness of the clustering. Higher values lead to more clusters. Multiple values will result in clustering being performed multiple times.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--input

-i

file

required

--modality

string

--obsp_connectivities

string

--output

-o

file

required

output

--obsm_name

string

--resolution

double

required

multiple

--output_compression

string