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.
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. |
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 v4.0.0 \
-main-script target/nextflow/cluster/leiden/main.nf \
-params-file params.yaml Relationships
Used by
Current component
Uses
No component dependencies found.