Lsi

Runs Latent Semantic Indexing.

Info

ID: lsi
Namespace: dimred

Links

Source

Computes cell embeddings, feature loadings and singular values. Uses the implementation of scipy

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 2.1.0 -latest \
  -main-script target/nextflow/dimred/lsi/main.nf \
  --help

Run command

Example of params.yaml

# Inputs
input: # please fill in - example: "input.h5mu"
modality: "atac"
# layer: "foo"
# var_input: "foo"

# LSI options
num_components: 50
scale_embeddings: true

# Outputs
# output: "$id.$key.output.h5mu"
output_compression: "gzip"
obsm_output: "X_lsi"
varm_output: "lsi"
uns_output: "lsi"
overwrite: false

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

# Arguments

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.0 -latest \
  -profile docker \
  -main-script target/nextflow/dimred/lsi/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 input h5mu file	file, required, example: "input.h5mu"
--modality	On which modality to run LSI on.	string, default: "atac"
--layer	Use specified layer for expression values. If not specified, uses adata.X.	string
--var_input	Column name in .var matrix that will be used to select which genes to run the LSI on. If not specified, uses all features.	string

LSI options

Name	Description	Attributes
--num_components	Number of components to compute.	integer, default: 50
--scale_embeddings	Scale embeddings to zero mean and unit variance.	boolean, default: TRUE

Outputs

Name	Description	Attributes
--output	Output h5mu file.	file, required, example: "output.h5mu"
--output_compression	The compression format to be used on the output h5mu object.	string, default: "gzip"
--obsm_output	In which .obsm slot to store the resulting embedding.	string, default: "X_lsi"
--varm_output	In which .varm slot to store the resulting loadings matrix.	string, default: "lsi"
--uns_output	In which .uns slot to store the stdev.	string, default: "lsi"
--overwrite	Allow overwriting .obsm, .varm and .uns slots.	boolean_true

Authors

• Sarah Ouologuem (contributor)

• Vladimir Shitov (contributor)