Initialize integration

Run calculations that output information required for most integration methods: PCA, nearest neighbour and UMAP.

Info

ID: initialize_integration
Namespace: integration/initialize_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 0.9.0 -latest \
  -main-script workflows/multiomics/integration/initialize_integration/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"

# PCA options
obsm_pca: "X_pca"
# var_pca_feature_selection: "foo"

# Neighbour calculation
uns_neighbors: "neighbors"
obsp_neighbor_distances: "distances"
obsp_neighbor_connectivities: "connectivities"

# Umap options
obsm_umap: "X_umap"

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

nextflow run openpipelines-bio/openpipeline \
  -r 0.9.0 -latest \
  -profile docker \
  -main-script workflows/multiomics/integration/initialize_integration/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"

PCA options

Name	Description	Attributes
--obsm_pca	In which .obsm slot to store the resulting PCA embedding.	string, default: "X_pca"
--var_pca_feature_selection	Column name in .var matrix that will be used to select which genes to run the PCA on.	string

Neighbour calculation

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

Umap options

Name	Description	Attributes
--obsm_umap	In which .obsm slot to store the resulting UMAP embedding.	string, default: "X_umap"

Authors

• Dries Schaumont (author)

Visualisation

flowchart LR
    p0(Input)
    p2(toSortedList)
    p4(flatMap)
    p12(pca)
    p22(find_neighbors)
    p32(umap)
    p40(Output)
    p0-->p2
    p2-->p4
    p4-->p12
    p12-->p22
    p22-->p32
    p32-->p40