runGiottoHarmony

run UMAP

runGiottoHarmony(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  vars_use = "list_ID",
  reduction = "cells",
  dim_reduction_to_use = "pca",
  dim_reduction_name = NULL,
  dimensions_to_use = 1:10,
  name = NULL,
  set_seed = TRUE,
  seed_number = 1234,
  toplevel_params = deprecated(),
  toplevel = 1L,
  return_gobject = TRUE,
  verbose = NULL,
  ...
)

Arguments

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

vars_use

character vector. Which variable(s) in metadata for harmony to remove

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

set_seed

use of seed

seed_number

seed number to use

toplevel_params

deprecated

toplevel

relative stackframe where call was made from

return_gobject

boolean: return giotto object (default = TRUE)

verbose

be verbose

...

additional HarmonyMatrix parameters

Value

giotto object with updated Harmony dimension reduction

Details

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

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : '/usr/bin/python3'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"

runGiottoHarmony(g, vars_use = "leiden_clus")
#> Error: package 'harmony' is not yet installed
#> 
#>  To install:
#> install.packages(c("harmony"))