runGiottoHarmony#

Last Updated: Sep 07, 2023

Description#

run UMAP

Usage#

runGiottoHarmony(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  vars_use = "list_ID",
  do_pca = FALSE,
  expression_values = c("normalized", "scaled", "custom"),
  reduction = "cells",
  dim_reduction_to_use = "pca",
  dim_reduction_name = NULL,
  dimensions_to_use = 1:10,
  name = NULL,
  feats_to_use = NULL,
  toplevel_params = 2,
  return_gobject = TRUE,
  verbose = NULL,
  ...
)

Arguments#

`gobject`	giotto object
`spat_unit`	spatial unit
`feat_type`	feature type
`vars_use`	If meta_data is dataframe, this defines which variable(s) to remove (character vector).
`do_pca`	Whether to perform PCA on input matrix.
`expression_values`	expression values to use
`reduction`	reduction on cells or features
`dim_reduction_to_use`	use another dimension reduction set as input
`dim_reduction_name`	name of dimension reduction set to use
`dimensions_to_use`	number of dimensions to use as input
`name`	arbitrary name for Harmony run
`feats_to_use`	if dim_reduction_to_use = NULL, which feats to use
`toplevel_params`	parameters to extract
`return_gobject`	boolean: return giotto object (default = TRUE)
`verbose`	be verbose
`...`	additional `HarmonyMatrix` parameters

Details#

This is a simple wrapper for the HarmonyMatrix function in the Harmony package doi:10.1038/s41592-019-0619-0.

Value#

giotto object with updated Harmony dimension recuction