Predict compound biotransformation pathways

epModel predicts the biotransformation pathway for a compound expressed with smiles using the selected model setting.

epModel(smiles, setting = NULL)

Arguments

smiles

Character vector. String specifying the smiles of a compound, which does not necessarily have to be available in enviPath.

setting

Character scalar. String specifying the unique identifier of a model setting. When null, the enviFormer setting is used. (Default: NULL)

Value

A list with two data frames with information on nodes and edges, respectively.

Examples

if( is_active ){
library(igraph)
library(ggraph)

# Perform login with your credentials
epLogin(username, password)

# Define smiles of interest
smiles <- "ClC(Cl)=C(Cl)Cl"

# Perform pathway prediction with enviFormer
former_out <- epModel(smiles)

# List available model settings
set_df <- epList("setting")

# View some model settings
head(set_df)

# Set id for PEPPER model setting
set_name <- "Global Setting - ECC and App Domain - PEPPER"
set_id <- set_df$id[set_df$name == set_name]

# Perform pathway prediction with PEPPER
pepper_out <- epModel(smiles, set_id)

# Convert model output to igraph object
path_graph <- graph_from_data_frame(
    pepper_out$edges,
    vertices = pepper_out$nodes
)

# Visualise predicted pathway
plot(path_graph)

# Visualise with ggraph
ggraph(path_graph, layout = "sugiyama") +
    geom_edge_link(
        aes(colour = probability),
        arrow = arrow(type = "closed")
    ) +
    geom_node_point(size = 3) +
    geom_node_text(aes(label = name), vjust = 2) +
    scale_edge_colour_continuous(
        limits = c(0, 1), low = "white", high = "red"
    ) +
    theme_graph(base_family = "")
}
#> 
#> Attaching package: ‘igraph’
#> The following objects are masked from ‘package:stats’:
#> 
#>     decompose, spectrum
#> The following object is masked from ‘package:base’:
#> 
#>     union
#> Loading required package: ggplot2
#> Hi nature lover, welcome to enviPath!