runGiottoHarmony: runGiottoHarmony

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

runGiottoHarmony

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 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41592-019-0619-0")}.

Value

giotto object with updated Harmony dimension recuction

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.