runSpatialDeconv#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_enrichment.R#L1953

Description#

Function to perform deconvolution based on single cell expression data

Usage#

runSpatialDeconv(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  deconv_method = c("DWLS"),
  expression_values = c("normalized"),
  logbase = 2,
  cluster_column = "leiden_clus",
  sign_matrix,
  n_cell = 50,
  cutoff = 2,
  name = NULL,
  return_gobject = TRUE
)

Arguments#

Argument

Description

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

deconv_method

method to use for deconvolution

expression_values

expression values to use

logbase

base used for log normalization

cluster_column

name of cluster column

sign_matrix

signature matrix for deconvolution

n_cell

number of cells per spot

cutoff

cut off (default = 2)

name

name to give to spatial deconvolution results

return_gobject

return giotto object

Value#

giotto object or deconvolution results

Seealso#

`runDWLSDeconv <#rundwlsdeconv>`__