exportGiottoViewer

compute highly variable genes

exportGiottoViewer(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  spat_loc_name = "raw",
  output_directory = NULL,
  spat_enr_names = NULL,
  factor_annotations = NULL,
  numeric_annotations = NULL,
  dim_reductions,
  dim_reduction_names,
  expression_values = c("scaled", "normalized", "custom"),
  dim_red_rounding = NULL,
  dim_red_rescale = c(-20, 20),
  expression_rounding = 2,
  overwrite_dir = TRUE,
  verbose = TRUE
)

Arguments

gobject

giotto object

spat_unit

spatial unit

feat_type

feature types

spat_loc_name

name of spatial locations to export

output_directory

directory where to save the files

spat_enr_names

spatial enrichment results to include for annotations

factor_annotations

giotto cell annotations to view as factor

numeric_annotations

giotto cell annotations to view as numeric

dim_reductions

high level dimension reductions to view

dim_reduction_names

specific dimension reduction names

expression_values

expression values to use in Viewer

dim_red_rounding

numerical indicating how to round the coordinates

dim_red_rescale

numericals to rescale the coordinates

expression_rounding

numerical indicating how to round the expression data

overwrite_dir

overwrite files in the directory if it already existed

verbose

be verbose

Value

writes the necessary output to use in Giotto Viewer

Details

Giotto Viewer expects the results from Giotto Analyzer in a specific format, which is provided by this function. To include enrichment results from createSpatialEnrich include the provided spatial enrichment name (default PAGE or rank) and add the gene signature names (.e.g cell types) to the numeric annotations parameter.