runPCA: runPCA

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

runPCA

Description

runs a Principal Component Analysis

Usage

runPCA(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  reduction = c("cells", "feats"),
  name = NULL,
  feats_to_use = "hvf",
  genes_to_use = NULL,
  return_gobject = TRUE,
  center = TRUE,
  scale_unit = TRUE,
  ncp = 100,
  method = c("irlba", "exact", "random", "factominer"),
  method_params = list(NA),
  rev = FALSE,
  set_seed = TRUE,
  seed_number = 1234,
  verbose = TRUE,
  ...
)

Arguments

gobject	giotto object
spat_unit	spatial unit
feat_type	feature type
expression_values	expression values to use
reduction	cells or genes
name	arbitrary name for PCA run
feats_to_use	subset of features to use for PCA
genes_to_use	deprecated use feats_to_use
return_gobject	boolean: return giotto object (default = TRUE)
center	center data first (default = TRUE)
scale_unit	scale features before PCA (default = TRUE)
ncp	number of principal components to calculate
method	which implementation to use
method_params	additional parameters
rev	do a reverse PCA
set_seed	use of seed
seed_number	seed number to use
verbose	verbosity of the function
...	additional parameters for PCA (see details)

Details

See runPCA and PCA for more information about other parameters.

• feats_to_use = NULL: will use all features from the selected matrix

• feats_to_use = <hvg name>: can be used to select a column name of highly variable features, created by (see calculateHVF)

• feats_to_use = c('geneA', 'geneB', ...): will use all manually provided features

Value

giotto object with updated PCA dimension recuction

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