Dimensionality reduction

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

Info

ID: dimensionality_reduction
Namespace: workflows/multiomics

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 2.1.1 -latest \
  -main-script target/nextflow/workflows/multiomics/dimensionality_reduction/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"
# pca_loadings_varm_output: "foo"
# pca_variance_uns_output: "foo"
pca_overwrite: false

# 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"

# Arguments

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.1 -latest \
  -profile docker \
  -main-script target/nextflow/workflows/multiomics/dimensionality_reduction/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`
`--pca_loadings_varm_output`	Name of the .varm key where the PCA loadings are stored.	`string`
`--pca_variance_uns_output`	Name of the .uns key where the variance and variance ratio will be stored as a map. The map will contain two keys: variance and variance_ratio respectively.	`string`
`--pca_overwrite`	Allow overwriting slots for PCA output.	`boolean_true`

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 TB
    v0(Channel.fromList)
    v2(filter)
    v10(filter)
    v18(pca)
    v25(cross)
    v35(cross)
    v41(filter)
    v195(concat)
    v50(filter)
    v65(cross)
    v75(cross)
    v84(branch)
    v111(concat)
    v96(cross)
    v106(cross)
    v115(branch)
    v142(concat)
    v127(cross)
    v137(cross)
    v146(branch)
    v173(concat)
    v158(cross)
    v168(cross)
    v180(cross)
    v190(cross)
    v202(cross)
    v209(cross)
    v221(cross)
    v228(cross)
    v232(Output)
    subgraph group_neighbors_leiden_umap [neighbors_leiden_umap]
        v58(find_neighbors)
        v89(leiden)
        v120(move_obsm_to_obs)
        v151(umap)
    end
    v84-->v111
    v115-->v142
    v146-->v173
    v0-->v2
    v2-->v10
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    v106-->v111
    v115-->v120
    v120-->v127
    v115-->v127
    v115-->v137
    v137-->v142
    v146-->v151
    v151-->v158
    v146-->v158
    v146-->v168
    v168-->v173
    v173-->v180
    v41-->v180
    v41-->v190
    v190-->v195
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    v2-->v202
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    v2-->v221
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    v228-->v232
    v35-->v41
    v18-->v35
    v58-->v75
    v75-->v84
    v89-->v106
    v111-->v115
    v120-->v137
    v142-->v146
    v151-->v168
    v173-->v190
    v195-->v221
    style group_neighbors_leiden_umap fill:#F0F0F0,stroke:#969696;
    style v0 fill:#e3dcea,stroke:#7a4baa;
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    style v25 fill:#e3dcea,stroke:#7a4baa;
    style v35 fill:#e3dcea,stroke:#7a4baa;
    style v41 fill:#e3dcea,stroke:#7a4baa;
    style v195 fill:#e3dcea,stroke:#7a4baa;
    style v50 fill:#e3dcea,stroke:#7a4baa;
    style v58 fill:#e3dcea,stroke:#7a4baa;
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