Viash Hub

Description

Calculate spatial autocorrelation for genes using Moran's I or Geary's C
on a precomputed spatial neighborhood graph. Allows identification of
spatially variable features.

Requires a spatial connectivities matrix in .obsp, e.g. produced by
squidpy.gr.spatial_neighbors or an equivalent GPU implementation.

The result is written to .uns as a DataFrame: moranI when --mode is
'moran', or gearyC when --mode is 'geary'.

Inputs

Name	Type & Properties	Description
--input -i	file required	Input h5mu file.
--modality	string	Which modality from the input MuData file to process.
--layer	string	Layer in the modality to use for the autocorrelation analysis. If unset, .X is used.
--obsp_connectivities	string	In which .obsp slot the spatial connectivities can be found.
--input_genes	string multiple	Subset of genes (from .var_names) to compute autocorrelation for. If unset, all genes in .var['highly_variable'] (if present) or all genes will be used.

Name

Type & Properties

--input

-i

file

required

--modality

string

--layer

string

--obsp_connectivities

string

--input_genes

string

multiple

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output h5mu file.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--output

-o

file

required

output

--output_compression

string

Options

Name	Type & Properties	Description
--mode	string	Spatial autocorrelation statistic to compute. 'moran' for Moran's I, 'geary' for Geary's C.
--n_perms	integer	Number of permutations for the permutation-based p-value calculation. If unset, only analytical p-values are computed.
--transformation	boolean	If true, row-normalize the connectivity matrix before computation.
--two_tailed	boolean_true	If set, compute two-tailed p-values from the permutation test instead of one-tailed.
--corr_method	string	Multiple-testing correction method to apply to p-values. Any method supported by `statsmodels.stats.multitest.multipletests`, e.g. 'fdr_bh', 'fdr_by', 'bonferroni', 'holm'. Pass an empty string to disable correction.
--use_sparse	boolean	If true, use a sparse representation of the expression matrix on the GPU.

Name

Type & Properties

--mode

string

--n_perms

integer

--transformation

boolean

--two_tailed

boolean_true

--corr_method

string

--use_sparse

boolean

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
obsp_connectivities: [ "spatial_connectivities" ]  
output: "$id.$key.output"  
mode: [ "moran" ]  
transformation: [ true ]  
corr_method: [ "fdr_bh" ]  
use_sparse: [ true ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_rapids.git \  
  -revision v0.1.3 \  
  -main-script target/nextflow/squidpy/spatial_autocorr/main.nf \  
  -params-file params.yaml

Relationships

Used by

1 relationships

wrappers/squidpy/spatial_autocorropenpipeline_rapids v0.1.3

Current component

squidpy/spatial_autocorropenpipeline_rapids v0.1.3

Uses

0 relationships

No component dependencies found.