Neighbors leiden umap

Performs neighborhood search, leiden clustering and run umap on an integrated embedding.

Info

ID: neighbors_leiden_umap
Namespace: workflows/multiomics

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.1 -latest \
  -main-script target/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf \
  --help

Run command

Example of params.yaml 
# Inputs
input: # please fill in - example: "dataset.h5mu"
obsm_input: # please fill in - example: "foo"
modality: "rna"

# Outputs
# output: "$id.$key.output.h5mu"

# Neighbour calculation
uns_neighbors: # please fill in - example: "foo"
obsp_neighbor_distances: # please fill in - example: "foo"
obsp_neighbor_connectivities: # please fill in - example: "foo"

# Clustering options
# obs_cluster: "foo"
leiden_resolution: [1.0]

# Umap options
# obsm_umap: "foo"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

# Arguments
nextflow run openpipelines-bio/openpipeline \
  -r 2.1.1 -latest \
  -profile docker \
  -main-script target/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf \
  -params-file params.yaml
Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups

Inputs

Name Description Attributes
--input Path to the sample. file, required, example: "dataset.h5mu"
--obsm_input The key of the embedding to use as input. string, required
--modality Which modality to process. string, default: "rna"

Outputs

Name Description Attributes
--output Destination path to the output. file, required, example: "output.h5mu"

Neighbour calculation

Name Description Attributes
--uns_neighbors In which .uns slot to store various neighbor output objects. string, required
--obsp_neighbor_distances In which .obsp slot to store the distance matrix between the resulting neighbors. string, required
--obsp_neighbor_connectivities In which .obsp slot to store the connectivities matrix between the resulting neighbors. string, required

Clustering options

Name Description Attributes
--obs_cluster Prefix for the .obs keys under which to add the cluster labels. Newly created columns in .obs will be created from the specified value for ‘–obs_cluster’ suffixed with an underscore and one of the resolutions resolutions specified in ‘–leiden_resolution’. string
--leiden_resolution Control the coarseness of the clustering. Higher values lead to more clusters. List of double, default: 1, multiple_sep: ";"

Umap options

Name Description Attributes
--obsm_umap In which .obsm slot to store the resulting UMAP embedding. When not specified, UMAP will not be executed. string

Authors

  • Dries Schaumont (author)

Visualisation

flowchart TB
    v0(Channel.fromList)
    v2(filter)
    v11(filter)
    v19(find_neighbors)
    v26(cross)
    v36(cross)
    v45(branch)
    v72(concat)
    v50(leiden)
    v57(cross)
    v67(cross)
    v76(branch)
    v103(concat)
    v81(move_obsm_to_obs)
    v88(cross)
    v98(cross)
    v107(branch)
    v134(concat)
    v112(umap)
    v119(cross)
    v129(cross)
    v141(cross)
    v148(cross)
    v160(cross)
    v167(cross)
    v171(Output)
    v45-->v72
    v76-->v103
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    v107-->v112
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    v107-->v129
    v129-->v134
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    v2-->v160
    v160-->v167
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    v167-->v171
    v19-->v36
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    v50-->v67
    v72-->v76
    v81-->v98
    v103-->v107
    v112-->v129
    v134-->v160
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