load previous HMRF
loadHMRF(
name_used = "test",
output_folder_used,
k_used = 10,
betas_used,
python_path_used
)
reloads a previous ran HMRF from doHRMF
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
#>
#> 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:
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