runGiottoHarmony#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/dimension_reduction.R#L1666

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#

Argument

Description

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` <#harmonymatrix>`__ parameters

Details#

This is a simple wrapper for the HarmonyMatrix function in the Harmony package c(“\Sexpr[results=rd]{tools:::Rd_expr_doi(“#1”)}?, “10.1038/s41592-019-0619-0?) list(“tools:::Rd_expr_doi(“10.1038/s41592-019-0619-0”)?) .

Value#

giotto object with updated Harmony dimension recuction