makeSignMatrixDWLS

Source: R/spatial_enrichment.R

Function to convert a matrix within a Giotto object into a format that can be used with runDWLSDeconv. A vector of cell types for cell_type_vector can be created from the cell metadata (pDataDT).

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

Arguments

gobject

Giotto object of single cell

expression_values

expression values to use

reverse_log

reverse a log-normalized expression matrix

log_base

the logarithm base (deafult = 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

See also

spatialDWLS