Totalvi leiden

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

Info

ID: totalvi_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 2.1.1 -latest \
  -main-script target/nextflow/workflows/integration/totalvi_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: "foo"
modality: "rna"
prot_modality: "prot"
reference: # please fill in - example: "path/to/file"

# Outputs
# output: "$id.$key.output.h5mu"
# reference_model_path: "totalvi_model_reference"
# query_model_path: "totalvi_model_query"

# General TotalVI Options
obs_batch: "sample_id"
max_epochs: 400
max_query_epochs: 200
weight_decay: 0.0
force_retrain: false
# var_input: "foo"

# TotalVI integration options RNA
rna_reference_modality: "rna"
rna_obsm_output: "X_totalvi"

# TotalVI integration options ADT
prot_reference_modality: "prot"
prot_obsm_output: "X_totalvi"

# Neighbour calculation RNA
rna_uns_neighbors: "totalvi_integration_neighbors"
rna_obsp_neighbor_distances: "totalvi_integration_distances"
rna_obsp_neighbor_connectivities: "totalvi_integration_connectivities"

# Neighbour calculation ADT
prot_uns_neighbors: "totalvi_integration_neighbors"
prot_obsp_neighbor_distances: "totalvi_integration_distances"
prot_obsp_neighbor_connectivities: "totalvi_integration_connectivities"

# Clustering options RNA
rna_obs_cluster: "totalvi_integration_leiden"
rna_leiden_resolution: [1.0]

# Clustering options ADT
prot_obs_cluster: "totalvi_integration_leiden"
prot_leiden_resolution: [1.0]

# Umap options
obsm_umap: "X_totalvi_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/integration/totalvi_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`
`--modality`	Which modality to process.	`string`, default: `"rna"`
`--prot_modality`	Which modality to process.	`string`, default: `"prot"`
`--reference`	Input h5mu file with reference data to train the TOTALVI model.	`file`, required

Outputs

Name	Description	Attributes
`--output`	Destination path to the output.	`file`, required, example: `"output.h5mu"`
`--reference_model_path`	Directory with the reference model. If not exists, trained model will be saved there	`file`, default: `"totalvi_model_reference"`
`--query_model_path`	Directory, where the query model will be saved	`file`, default: `"totalvi_model_query"`

General TotalVI Options

Name	Description	Attributes
`--obs_batch`	.Obs column name discriminating between your batches.	`string`, default: `"sample_id"`
`--max_epochs`	Number of passes through the dataset	`integer`, default: `400`
`--max_query_epochs`	Number of passes through the dataset, when fine-tuning model for query	`integer`, default: `200`
`--weight_decay`	Weight decay, when fine-tuning model for query	`double`, default: `0`
`--force_retrain`	If true, retrain the model and save it to reference_model_path	`boolean_true`
`--var_input`	Boolean .var column to subset data with (e.g. containing highly variable genes). By default, do not subset genes.	`string`

TotalVI integration options RNA

Name	Description	Attributes
`--rna_reference_modality`		`string`, default: `"rna"`
`--rna_obsm_output`	In which .obsm slot to store the normalized RNA from TOTALVI.	`string`, default: `"X_totalvi"`

TotalVI integration options ADT

Name	Description	Attributes
`--prot_reference_modality`	Name of the modality containing proteins in the reference	`string`, default: `"prot"`
`--prot_obsm_output`	In which .obsm slot to store the normalized protein data from TOTALVI.	`string`, default: `"X_totalvi"`

Neighbour calculation RNA

Name	Description	Attributes
`--rna_uns_neighbors`	In which .uns slot to store various neighbor output objects.	`string`, default: `"totalvi_integration_neighbors"`
`--rna_obsp_neighbor_distances`	In which .obsp slot to store the distance matrix between the resulting neighbors.	`string`, default: `"totalvi_integration_distances"`
`--rna_obsp_neighbor_connectivities`	In which .obsp slot to store the connectivities matrix between the resulting neighbors.	`string`, default: `"totalvi_integration_connectivities"`

Neighbour calculation ADT

Name	Description	Attributes
`--prot_uns_neighbors`	In which .uns slot to store various neighbor output objects.	`string`, default: `"totalvi_integration_neighbors"`
`--prot_obsp_neighbor_distances`	In which .obsp slot to store the distance matrix between the resulting neighbors.	`string`, default: `"totalvi_integration_distances"`
`--prot_obsp_neighbor_connectivities`	In which .obsp slot to store the connectivities matrix between the resulting neighbors.	`string`, default: `"totalvi_integration_connectivities"`

Clustering options RNA

Name	Description	Attributes
`--rna_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: `"totalvi_integration_leiden"`
`--rna_leiden_resolution`	Control the coarseness of the clustering. Higher values lead to more clusters.	List of `double`, default: `1`, multiple_sep: `";"`

Clustering options ADT

Name	Description	Attributes
`--prot_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: `"totalvi_integration_leiden"`
`--prot_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_totalvi_umap"`

Authors

Dries Schaumont (author)

Visualisation

flowchart TB
    v0(Channel.fromList)
    v2(filter)
    v10(filter)
    v18(totalvi)
    v25(cross)
    v35(cross)
    v41(filter)
    v50(filter)
    v65(cross)
    v75(cross)
    v84(branch)
    v111(concat)
    v96(cross)
    v106(cross)
    v115(branch)
    v142(concat)
    v127(cross)
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    v146(branch)
    v173(concat)
    v158(cross)
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    v180(cross)
    v190(cross)
    v196(filter)
    v350(concat)
    v205(filter)
    v220(cross)
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    v239(branch)
    v266(concat)
    v251(cross)
    v261(cross)
    v270(branch)
    v297(concat)
    v282(cross)
    v292(cross)
    v301(branch)
    v328(concat)
    v313(cross)
    v323(cross)
    v335(cross)
    v345(cross)
    v357(cross)
    v364(cross)
    v376(cross)
    v383(cross)
    v387(Output)
    subgraph group_rna_neighbors_leiden_umap [rna_neighbors_leiden_umap]
        v58(find_neighbors)
        v89(leiden)
        v120(move_obsm_to_obs)
        v151(umap)
    end
    subgraph group_adt_neighbors_leiden_umap [adt_neighbors_leiden_umap]
        v213(find_neighbors)
        v244(leiden)
        v275(move_obsm_to_obs)
        v306(umap)
    end
    v84-->v111
    v115-->v142
    v146-->v173
    v239-->v266
    v270-->v297
    v301-->v328
    v0-->v2
    v2-->v10
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    v137-->v142
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    v111-->v115
    v120-->v137
    v142-->v146
    v151-->v168
    v173-->v190
    v213-->v230
    v230-->v239
    v244-->v261
    v266-->v270
    v275-->v292
    v297-->v301
    v306-->v323
    v328-->v345
    v350-->v376
    style group_rna_neighbors_leiden_umap fill:#F0F0F0,stroke:#969696;
    style group_adt_neighbors_leiden_umap fill:#F0F0F0,stroke:#969696;
    style v0 fill:#e3dcea,stroke:#7a4baa;
    style v2 fill:#e3dcea,stroke:#7a4baa;
    style v10 fill:#e3dcea,stroke:#7a4baa;
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