Run HMRF
doHMRF( gobject, expression_values = c("normalized", "scaled", "custom"), spatial_network_name = "Delaunay_network", 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 )
| gobject | giotto object |
|---|---|
| expression_values | expression values to use |
| spatial_network_name | name of spatial network to use for HMRF |
| 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 |
Creates a directory with results that can be viewed with viewHMRFresults
Description of HMRF parameters ...