calculate_interaction_score: [INTERNAL] Calls a python script to calculate interaction score for combined graphs

Description

[INTERNAL] The interaction score is computed and saved in an additional `interaction_weight` edge attribute. This function expects the combined graphs for both groups along with their corresponding drug target and node lists to be saved at `saving_path`. Graphs and drug targets should be weighted edge lists in `gml` and `tsv` format, respectively. Node files should contain one node id per line. The script for calculating the interaction score is called with `python_executable`. An alternate script can be specified with `script_path`. The score for an edge is computed as the sum of the average product of weights along all simple paths of length l (over all path lengths up to `max_path_length`) between the source and target node of the edge.

Usage

calculate_interaction_score(
  max_path_length,
  total_edges,
  saving_path,
  conda = FALSE,
  script_path = NULL,
  int_score_mode = "auto",
  cluster_address = "auto",
  graphB_null = FALSE
)

Value

Does not return anything, instead calls Python script which outputs `gml` files

Arguments

max_path_length: [int] Integer of maximum length of simple paths to include in the generate_interaction_score_graphs computation. (default: 3)
total_edges: Vector with total edges in each group
saving_path: [string] Path to save intermediate output of DrDimont's functions. Default is current working directory. Directory to use for writing intermediate data when passing input and output between Python and R.
conda: [bool] Specifying if python is installed in a conda environment. Set TRUE if python is installed with conda, else python dependencies are assumed to be installed with pip. (default: FALSE)
script_path: [string] Path to the interaction score Python script. Set NULL to use package internal script (default).
int_score_mode: ["auto"|"sequential"|"ray"] Whether to compute interaction score in parallel using the Ray python library or sequentially. When `auto` it depends on the graph sizes. (default: "auto")
cluster_address: [string] Local node IP-address of Ray if executed on a cluster. On a cluster: Start ray with ray start --head --num-cpus 32 on the console before DrDimont execution. It should work with "auto", if it does not specify IP-address given by the ray start command. (default: "auto")
graphB_null: [bool] Specifying if graphB of `groupB` is given (FALSE) or not (TRUE). (default: FALSE)