feature_annotation/spatial_autocorr

Description

Calculate spatial autocorrelation for genes using Moran's I or Geary's C.
This allows identifying spatially variable genes.

Type

python_script

Links

Repository

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
obsp_neighborhood_graph: [ "spatial_connectivities" ]  
use_all_genes: [ false ]  
mode: [ "moran" ]  
attr: [ "X" ]  
n_perms: [ 100 ]  
use_raw: [ false ]  
output: "$id.$key.output"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/feature_annotation/spatial_autocorr/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Input h5mu file.
--modality	string	Modality to use.
--layer	string	Layer in the AnnData object to use. - If `attr` is 'X', this is the key in `.layers` to use. If not provided, `.X` is used. - If `attr` is 'obsm', this is the key in `.obsm` to use.
--input_genes	string multiple	The features to calculate autocorrelation for. Meaning depends on `--attr`: - If `attr` is 'X' (default), this must be a list of gene names from `.var_names`. If not provided, it defaults to using genes in `.var['highly_variable']` (if present), or all genes. This behavior can be overridden by setting `--use_all_genes` to `true`. Note: You cannot pass a column name from `.var` here. - If `attr` is 'obs', this must be a list of column names from `.obs`. - If `attr` is 'obsm', this must be indices in `.obsm[layer]` (as strings).
--obsp_neighborhood_graph	string	Key in .obsp where spatial connectivities are stored.
--use_all_genes	boolean	Whether to use all genes even if highly variable genes are present in .var. If set to true, all genes will be used.

Name

Type & Properties

--input

file

required

--modality

string

--layer

string

--input_genes

string

multiple

--obsp_neighborhood_graph

string

--use_all_genes

boolean

Parameters

Name	Type & Properties	Description
--mode	string	Mode of spatial autocorrelation.
--attr	string	The attribute of the AnnData object to use for calculation. - 'X': Use gene expression data (default). - 'obs': Use cell metadata. - 'obsm': Use multidimensional embeddings.
--n_perms	integer	Number of permutations for p-value calculation.
--use_raw	boolean	Whether to use .raw attribute of AnnData.

Name

Type & Properties

--mode

string

--attr

string

--n_perms

integer

--use_raw

boolean

Outputs

Name	Type & Properties	Description
--output	file required output	Output h5mu file with results in .uns.

Name

Type & Properties

--output

file

required

output