Run Iterative Latent Semantic Indexing (LSI)

Performs Iterative LSI on a Giotto object, replicating ArchR's approach using Giotto functions.

runIterativeLSI(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = "raw",
  name = NULL,
  feats_to_use = NULL,
  return_gobject = TRUE,
  iterations = 2,
  sample_cells_pre = 10000,
  sample_cells_final = NULL,
  var_features = 25000,
  dims = 1:30,
  scale_to = 10000,
  lsi_method = 2,
  resolution = 2,
  first_selection = "top",
  k = 10,
  seed = 1234,
  set_seed = TRUE,
  cor_cutoff = 0.75,
  verbose = NULL
)

Arguments

gobject

Giotto object

spat_unit

Spatial unit (e.g., "cell")

feat_type

Feature type (e.g., "spatial_atac")

expression_values

Values to use (e.g., "raw")

name

Name for reduction (default: feat_type + "_iterative_lsi")

feats_to_use

Initial feature subset (NULL = all)

return_gobject

Return Giotto object (default = TRUE)

iterations

Number of iterations (default = 2)

sample_cells_pre

Cells to subsample in early iterations

sample_cells_final

Cells to subsample in final iteration (NULL = all)

var_features

Number of variable features (default = 25000)

dims

Vector of LSI dimensions to use for clustering and projection steps (default = 1:30)

scale_to

TF-IDF scaling factor for sub_method 2 (default = 10000)

lsi_method

TF-IDF method: 1 = Casanovich, 2 = Stuart, 3 = ArchR, 4 = Giotto (default = 3). See [Giotto::norm_tfidf] for more information on how each of these are calculated.

resolution

Clustering resolution (default = 2)

first_selection

"top" (accessibility) or "var" (variance) (default = "var")

k

Number of nearest neighbors for sNN (default = 10)

seed

Seed for reproducibility (default = 1234)

set_seed

Logical, whether to set a seed (default = TRUE)

cor_cutoff

Correlation cutoff for filtering LSI dimensions correlated with sequencing depth in intermediate steps (default = 0.75)

verbose

Verbosity (default = NULL, inherits from gobject)

Value

Giotto object or LSI coordinates