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Deconvolute with DOT

deconvolute_dot.Rd

Runs DOT deconvolution and returns the DOT weight matrix with column names prefixed by result_name.

Usage 

deconvolute_dot(
  single_cell_obj,
  spatial_obj,
  cell_type_col = "cell_ontology_class",
  assay_sc = "counts",
  assay_sp = "counts",
  result_name = "dot",
  ratios_weight = 0,
  max_spot_size = 20,
  ...
)

Arguments

single_cell_obj

SingleCellExperiment.

spatial_obj

SpatialExperiment.

cell_type_col

Column in single_cell_obj containing cell type labels.

assay_sc

Single-cell assay to use.

assay_sp

Spatial assay to use.

result_name

Prefix used to label result columns (default: "dot").

ratios_weight

Strength of matching cell-type ratios between scRNA-seq and spatial data (default: 0).

max_spot_size

Maximum number of cells per spot (platform dependent).

...

Additional parameters passed to DOT setup/run functions.