add_edge_attributes_from_data.frame: Add edge attributes to 'igraph' object from 'data.frame'

In michaelwitting/wormLipidPredictR: Lipid reaction prediction based on WormJam

Add edge attributes to igraph object from data.frame

Description

The function adds edge weights to a igraph object g. The weights are stored in the attributes object. The function will return a igraph object with updated edge weights.

The attributes object is a data.frame.

The data.frame contains the columns vertex, a character vector of length 2, specifying the out- and ingoing vertices for the edge and the edge weights in the remaining columns. The weights will be stored in the respective slots with same names as the colnames of attributes of the returned igraph object.#'

Usage

add_edge_attributes_from_data.frame(
  g,
  attributes,
  column_from = "from",
  column_to = "to"
)

Arguments

g	igraph object
attributes	data.frame containing edge attribute information
column_from	chararacter of length 1, specifying the columns containing the outgoing vertices in attributes of type data.frame
column_to	chararacter of length 1, specifying the columns containing the ingoing vertices in attributes of type data.frame

Details

vertex has to be adjusted to the attributes object. The character of length 2 will specify the columns containing the out- and ingoing vertices of the graph.

Value

igraph object

Author(s)

Thomas Naake, [e-mail]

Examples

FA <- c("FA 12:0", "FA 14:0", "FA 16:0")

## create data.frame with reactions and reaction order
reactions <- rbind(
    c(1, "RHEA:15421", "M_ATP + M_CoA + M_FA = M_PPi + M_AMP + M_AcylCoA", FALSE),
    c(2, "RHEA:15325", "M_Glycerol-3-P + M_AcylCoA = M_CoA + M_LPA", FALSE),
    c(3, "RHEA:19709", "M_AcylCoA + M_LPA = M_CoA + M_PA", FALSE),
    c(4, "RHEA:27429", "M_H2O + M_PA = M_Pi + M_1,2-DG", FALSE)
)
reactions <- data.frame(order = reactions[, 1], reaction_RHEA = reactions[, 2],
    reaction_formula = reactions[, 3], directed = reactions[, 4])
reactions$order <- as.numeric(reactions$order)
reactions$directed <- as.logical(reactions$directed)

## create the list with reactions
reaction_l <- create_reactions(substrates = list(FA = FA), reactions = reactions)

## create the adjacency matrix
reaction_adj <- create_reaction_adjacency_matrix(reaction_l)

## create graph
g <- igraph::graph_from_adjacency_matrix(reaction_adj, mode = "directed", weighted = TRUE)

## attributes: data.frame
attributes <- data.frame(
    rbind(
        c("CoA 12:0", "PA 12:0/0:0", 0.5),
        c("CoA 12:0", "PA 14:0/12:0", 0.8)
))
names(attributes) <- c("from", "to", "weight")
attributes$weight <- as.numeric(attributes$weight)

## apply the function
LipidNetworkPredictR:::add_edge_attributes_from_data.frame(g, attributes, column_from = "from", 
    column_to = "to")

michaelwitting/wormLipidPredictR documentation built on April 17, 2025, 7:27 p.m.