doHMRF | R Documentation |
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 |
Description of HMRF parameters ...
Creates a directory with results that can be viewed with viewHMRFresults
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