loadHMRF

load previous HMRF

loadHMRF(
  name_used = "test",
  output_folder_used,
  k_used = 10,
  betas_used,
  python_path_used
)

Arguments

name_used

name of HMRF that was run

output_folder_used

output folder that was used

k_used

number of HMRF domains that was tested

betas_used

betas that were tested

python_path_used

python path that was used

Value

reloads a previous ran HMRF from doHRMF

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"
x <- tempdir()
doHMRF(g,
    spatial_genes = c("Gna12", "Ccnd2"), output_folder = x,
    betas = c(0, 2, 50)
)
#> 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)

loadHMRF(
    output_folder_used = x, betas_used = c(0, 2, 50),
    python_path_used = NULL
)
#> Error in loadHMRF(output_folder_used = x, betas_used = c(0, 2, 50), python_path_used = NULL): 
#>  doHMRF was not run in this output directory