exportGiottoViewer#

Last Updated: Jan 29, 2024

Description#

compute highly variable genes

Usage#

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 = T
)

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

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.

Value#

writes the necessary output to use in Giotto Viewer

Examples#

## Not run:

data(mini_giotto_single_cell)
exportGiottoViewer(mini_giotto_single_cell)

## End(Not run)