wrappers/squidpy/spatial_autocorr

Description

Calculate spatial autocorrelation (Moran's I or Geary's C) for genes on a
precomputed spatial neighborhood graph, running either the GPU
(rapids-singlecell) or the CPU (squidpy) variant, selected with --device_type.

Inputs

Name	Type & Properties	Description
--input	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, highly variable genes (if annotated) or all genes are used.

Name

Type & Properties

--input

file

required

--modality

string

--layer

string

--obsp_connectivities

string

--input_genes

string

multiple

Compute

Name	Type & Properties	Description
--device_type	string	Which implementation to run: the GPU (rapids-singlecell) variant or the CPU (scanpy/squidpy) variant of the component. Selecting `gpu` requires a CUDA-capable GPU; the component errors out if none is available (there is no automatic fallback to CPU).

Name

Type & Properties

--device_type

string

Outputs

Name	Type & Properties	Description
--output	file required output	Output h5mu file.

Name

Type & Properties

--output

file

required

output

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.

Name

Type & Properties

--mode

string

--n_perms

integer

rapids-singlecell options

Name	Type & Properties	Description
--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 multipletests, e.g. 'fdr_bh', 'bonferroni'). Pass an empty string to disable correction.
--use_sparse	boolean	If true, use a sparse representation of the expression matrix on the GPU.
--output_compression	string	The compression format to be used on the output h5mu object.

Name

Type & Properties

--transformation

boolean

--two_tailed

boolean_true

--corr_method

string

--use_sparse

boolean

--output_compression

string

Squidpy options

Name	Type & Properties	Description
--use_all_genes	boolean	Use all genes even if highly variable genes are annotated in .var.
--attr	string	Which AnnData attribute --input_genes refers to (X uses .var_names, obs uses .obs columns, obsm uses indices in .obsm[layer]).
--use_raw	boolean	Whether to use .raw for the expression values.

Name

Type & Properties

--use_all_genes

boolean

--attr

string

--use_raw

boolean

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
obsp_connectivities: [ "spatial_connectivities" ]  
device_type: [ "gpu" ]  
output: "$id.$key.output.h5mu"  
mode: [ "moran" ]  
transformation: [ true ]  
corr_method: [ "fdr_bh" ]  
use_sparse: [ true ]  
use_all_genes: [ false ]  
attr: [ "X" ]  
use_raw: [ false ]  
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/wrappers/squidpy/spatial_autocorr/main.nf \  
  -params-file params.yaml

wrappers/squidpy/spatial_autocorr

Inputs

Compute

Outputs

Options

rapids-singlecell options

Squidpy options

Run this component

Relationships

Used by

Uses