Harmony leiden

Run harmony integration followed by neighbour calculations, leiden clustering and run umap on the result.

Info

ID: harmony_leiden
Namespace: workflows/integration

Links

Source

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 1.0.1 -latest \
  -main-script target/nextflow/workflows/integration/harmony_leiden/main.nf \
  --help

Run command

Example of params.yaml

# Inputs
id: # please fill in - example: "foo"
input: # please fill in - example: "dataset.h5mu"
layer: "log_normalized"
modality: "rna"

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

# Neighbour calculation
uns_neighbors: "harmonypy_integration_neighbors"
obsp_neighbor_distances: "harmonypy_integration_distances"
obsp_neighbor_connectivities: "harmonypy_integration_connectivities"

# Harmony integration options
embedding: "X_pca"
obsm_integrated: "X_pca_integrated"
obs_covariates: # please fill in - example: ["batch", "sample"]
theta: [2]

# Clustering options
obs_cluster: "harmony_integration_leiden"
leiden_resolution: [1]

# Umap options
obsm_umap: "X_leiden_harmony_umap"

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

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -profile docker \
  -main-script target/nextflow/workflows/integration/harmony_leiden/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
--id	ID of the sample.	string, required, example: "foo"
--input	Path to the sample.	file, required, example: "dataset.h5mu"
--layer	use specified layer for expression values instead of the .X object from the modality.	string, default: "log_normalized"
--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, default: "harmonypy_integration_neighbors"
--obsp_neighbor_distances	In which .obsp slot to store the distance matrix between the resulting neighbors.	string, default: "harmonypy_integration_distances"
--obsp_neighbor_connectivities	In which .obsp slot to store the connectivities matrix between the resulting neighbors.	string, default: "harmonypy_integration_connectivities"

Harmony integration options

Name	Description	Attributes
--embedding	Embedding to use as input	string, default: "X_pca"
--obsm_integrated	In which .obsm slot to store the resulting integrated embedding.	string, default: "X_pca_integrated"
--obs_covariates	The .obs field(s) that define the covariate(s) to regress out.	List of string, required, example: "batch", "sample", multiple_sep: ";"
--theta	Diversity clustering penalty parameter. Specify for each variable in group.by.vars. theta=0 does not encourage any diversity. Larger values of theta result in more diverse clusters.”	List of double, default: 2, multiple_sep: ";"

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, default: "harmony_integration_leiden"
--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.	string, default: "X_leiden_harmony_umap"

Authors

• Dries Schaumont (author)

Visualisation

flowchart TB
    v0(Channel.fromList)
    v18(harmonypy)
    v49(concat)
    v38(find_neighbors)
    v59(leiden)
    v79(move_obsm_to_obs)
    v92(mix)
    v101(umap)
    v128(Output)
    v0-->v18
    v18-->v38
    v38-->v49
    v49-->v59
    v59-->v79
    v79-->v92
    v49-->v92
    v92-->v101
    v101-->v128
    style v0 fill:#e3dcea,stroke:#7a4baa;
    style v18 fill:#e3dcea,stroke:#7a4baa;
    style v49 fill:#e3dcea,stroke:#7a4baa;
    style v38 fill:#e3dcea,stroke:#7a4baa;
    style v59 fill:#e3dcea,stroke:#7a4baa;
    style v79 fill:#e3dcea,stroke:#7a4baa;
    style v92 fill:#e3dcea,stroke:#7a4baa;
    style v101 fill:#e3dcea,stroke:#7a4baa;
    style v128 fill:#e3dcea,stroke:#7a4baa;