doHMRF

Run HMRF

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

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

Value

Creates a directory with results that can be viewed with viewHMRFresults

Details

Description of HMRF parameters ...

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"
spat_genes <- binSpect(g)
#> 
#> This is the single parameter version of binSpect
#> 
#> 1. matrix binarization complete
#> 
#> 2. spatial enrichment test completed
#> 
#> 3. (optional) average expression of high
#>  expressing cells calculated
#> 
#> 4. (optional) number of high expressing cells
#>  calculated

doHMRF(g,
    spatial_genes = spat_genes[seq_len(10)]$feats,
    output_folder = tempdir()
)
#> Error: package 'smfishHmrf' is not yet installed
#> 
#>  To install:
#> ## active python env: '/usr/bin/python3' 
#> ## python version: 3.10
#> ## restart session then use GiottoClass::set_giotto_python_path() if this is incorrect
#> reticulate::conda_install(envname = '/usr/bin/python3', packages = c('smfishHmrf'), pip = TRUE)