doHMRF

doHMRF

Description

Run HMRF

Usage

doHMRF(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  spatial_network_name = "Delaunay_network",
  spat_loc_name = "raw",
  spatial_genes = NULL,
  spatial_dimensions = c("sdimx", "sdimy", "sdimz"),
  dim_reduction_to_use = NULL,
  dim_reduction_name = "pca",
  dimensions_to_use = 1:10,
  seed = 100,
  name = "test",
  k = 10,
  betas = c(0, 2, 50),
  tolerance = 1e-10,
  zscore = c("none", "rowcol", "colrow"),
  numinit = 100,
  python_path = NULL,
  output_folder = NULL,
  overwrite_output = TRUE
)

Arguments

Argument	Description
gobject	giotto object
spat_unit	spatial unit
feat_type	feature type
expression_values	expression values to use
spatial_network_name	name of spatial network to use for HMRF
spat_loc_name	name of spatial locations
spatial_genes	spatial genes to use for HMRF
spatial_dimensions	select spatial dimensions to use, default is all possible dimensions
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
seed	seed to fix random number generator (for creating initialization of HMRF) (-1 if no fixing)
name	name of HMRF run
k	number of HMRF domains
betas	betas to test for. three numbers: start_beta, beta_increment, num_betas e.g. c(0, 2.0, 50)
tolerance	tolerance
zscore	zscore
numinit	number of initializations
python_path	python path to use
output_folder	output folder to save results
overwrite_output	overwrite output folder

Details

Description of HMRF parameters …

Value

Creates a directory with results that can be viewed with viewHMRFresults