runONTraCV1

run ONTraC

runONTraCV1(
  ONTraC_input,
  dataset,
  preprocessing_dir,
  GNN_dir,
  NTScore_dir,
  n_cpu = 4L,
  n_neighbors = 50L,
  n_local = 20L,
  device = c("cpu", "cuda"),
  epochs = 1000L,
  patience = 100L,
  min_delta = 0.001,
  min_epochs = 50L,
  batch_size = 0L,
  seed = 42L,
  lr = 0.03,
  hidden_feats = 4L,
  k = 6L,
  modularity_loss_weight = 0.3,
  purity_loss_weight = 300,
  regularization_loss_weight = 0.1,
  beta = 0.03,
  python_path = "giotto_ontrac_env"
)

Arguments

dataset

the path to the input data file

preprocessing_dir

the directory to save the preprocessing results

GNN_dir

the directory to save the GNN results

NTScore_dir

the directory to save the NTScore results

n_cpu

the number of CPUs used for niche network constructing. Default is 4L

n_neighbors

the number of neighbors used for ONTraC in niche network construction. Default is 50L

n_local

the index of local neighbor used for ONTraC in niche network construction for normalization. Default is 20L

device

the device used for ONTraC running GNN model. Default is "cpu"

epochs

the maximum number of epochs for model training. Default is 1000L

patience

the number of epochs wait for better result. Default is 100L

min_delta

the minimum change of loss to be considered as improvement. Default is 0.001

min_epochs

the minimum number of epochs to train. Default is 50L

batch_size

the batch size for training. Default is 0L for whole dataset

seed

the random seed for reproducibility. Default is 42L

lr

the learning rate for training. Default is 0.03

hidden_feats

the number of hidden features for GNN model. Default is 4L

k

the number of neighbors for GNN model. Default is 6L

modularity_loss_weight

the weight of modularity loss. Default is 0.3

purity_loss_weight

the weight of purity loss. Default is 300.0

regularization_loss_weight

the weight of regularization loss. Default is 0.1

beta

the weight of entropy loss. Default is 0.03

python_path,

path to python executable within a conda/miniconda environment. Default is "giotto_ontrac_env"

Value

none

Details

This function runs ONTraC

Examples

runONTraCV1(
    dataset = "ONTraC_dataset_input.csv",
    preprocessing_dir = "preprocessing_dir",
    GNN_dir = "GNN_dir",
    NTScore_dir = "NTScore_dir",
    envname = "giotto_ontrac_env"
)
#> Error in runONTraCV1(dataset = "ONTraC_dataset_input.csv", preprocessing_dir = "preprocessing_dir",     GNN_dir = "GNN_dir", NTScore_dir = "NTScore_dir", envname = "giotto_ontrac_env"): unused argument (envname = "giotto_ontrac_env")