Run official Python COMMOT in an isolated subprocess. Raw expression, metadata, and raw coordinates are exchanged through files; AnnData is not placed inside the Seurat object.
Usage
RunCOMMOT(
object,
group.by,
species = c("human", "mouse"),
database = "CellChat",
assay = NULL,
layer = "counts",
image = NULL,
coord.cols = c("col", "row"),
distance.threshold = NULL,
cluster = FALSE,
direction = FALSE,
communication.args = list(),
cluster.args = list(),
direction.args = list(),
result.name = "default",
envname = "commot_env",
output.dir = NULL,
store.h5ad = FALSE,
overwrite = FALSE,
backend = c("cpp", "r"),
verbose = TRUE,
srt = NULL
)Arguments
- object
A `Seurat` spatial object.
- group.by
Metadata column used to aggregate communication by group.
- species
COMMOT ligand-receptor database species.
- database
Official COMMOT ligand-receptor database name.
- assay, layer
Assay and raw-count layer.
- image
Explicit spatial image. Required for multi-image objects.
- coord.cols
Metadata coordinate columns used when no image is present.
- distance.threshold
Maximum signaling distance in raw-coordinate units.
- cluster
Whether to run official cluster communication permutations.
- direction
Whether to run official communication direction analysis.
- communication.args
Named arguments for official spatial communication. Runner-only fields are `normalize`, `target_sum`, `signaling_type`, and nested `filter_args`.
- cluster.args
Named arguments for official cluster communication.
- direction.args
Named arguments for official communication direction.
- result.name
Stored result name.
- envname
Isolated Python environment name.
- output.dir
External directory for a requested H5AD artifact.
- store.h5ad
Whether to retain the complete AnnData as an external H5AD.
- overwrite
Whether to replace an existing named result or H5AD artifact.
- backend
Post-processing engine used for SCOP CCC result aggregation.
- verbose
Whether to print progress messages.
- srt
Deprecated alias for `object`; supply exactly one of the two. It will be removed in scop 1.0.0.