spatialAEH

Compute spatial variable genes with spatialDE method

spatialAEH(
  gobject = NULL,
  feat_type = NULL,
  spat_unit = NULL,
  spat_loc_name = "raw",
  SpatialDE_results = NULL,
  name_pattern = "AEH_patterns",
  expression_values = c("raw", "normalized", "scaled", "custom"),
  pattern_num = 6,
  l = 1.05,
  python_path = NULL,
  return_gobject = TRUE
)

Arguments

gobject

Giotto object

feat_type

feature type

spat_unit

spatial unit

spat_loc_name

name for spatial locations

SpatialDE_results

results of spatialDE function

name_pattern

name for the computed spatial patterns

expression_values

gene expression values to use

pattern_num

number of spatial patterns to look for

l

lengthscale

python_path

specify specific path to python if required

return_gobject

show plot

Value

An updated giotto object

Details

This function is a wrapper for the SpatialAEH method implemented in the ...

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : '/usr/bin/python3'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"

spatialAEH(g)
#> Error in py_run_file_impl(file, local, convert): ModuleNotFoundError: No module named 'pandas'
#> Run `reticulate::py_last_error()` for details.