spatialAEH#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_genes.R#L1994

Description#

Compute spatial variable genes with spatialDE method

Usage#

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#

Argument

Description

gobject

Giotto object

feat_type

feature type

spat_unit

spatial unit

spat_loc_name

name for spatial locations

SpatialDE_results

results of `spatialDE <#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

Details#

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

Value#

An updated giotto object