makeSignMatrixDWLS#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_enrichment.R#L120

Description#

Function to convert a matrix within a Giotto object into a format that can be used with `runDWLSDeconv <#rundwlsdeconv>`__ for deconvolution. A vector of cell types for parameter cell_type_vector can be created from the cell metadata ( `pDataDT <#pdatadt>`__ ).

Usage#

makeSignMatrixDWLS(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  reverse_log = TRUE,
  log_base = 2,
  sign_gene,
  cell_type_vector,
  cell_type = NULL
)

Arguments#

Argument

Description

gobject

Giotto object of single cell

spat_unit

spatial unit

feat_type

feature type to use

expression_values

expression values to use

reverse_log

reverse a log-normalized expression matrix

log_base

the logarithm base (default = 2)

sign_gene

all of DE genes (signature)

cell_type_vector

vector with cell types (length = ncol(matrix))

cell_type

deprecated, use cell_type_vector

Value#

matrix

Seealso#

`runDWLSDeconv <#rundwlsdeconv>`__