doHMRF#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/python_hmrf.R#L29

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