add_edge_attributes: Add edge attributes to 'igraph' object

In michaelwitting/wormLipidPredictR: Lipid reaction prediction based on WormJam

Add edge attributes to igraph object

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 can be either a matrix or a data.frame.

The matrix is an adjacency matrix containing as entries the weights. The weights will be stored in the E(g)$value slot of the returned igraph object.

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(g, attributes, cols_vertex = colnames(attributes)[1:2])

Arguments

g	igraph object
attributes	matrix or data.frame containing edge attribute information
cols_vertex	chararacter of length 2, specifying the columns containing the out- and ingoing vertices in attributes of type data.frame

Details

cols_vertex has to be adjusted only when attributes is a data.frame. The character of length 2 will specify the columns containing the out- and ingoing vertices of the graph.

In case of attributes is a matrix, the matrix entries will be stored in E(g)$value

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
add_edge_attributes(g, attributes, cols_vertex = c("from", "to"))

## attributes: matrix
attributes <- matrix(c(0, 0.5, 0.8, 0, 0, 0, 0, 0, 0), ncol = 3, byrow = TRUE, 
    dimnames = list(
        c("CoA(12:0)", "PA(12:0/0:0)", "PA(14:0/12:0)"),
        c("CoA(12:0)", "PA(12:0/0:0)", "PA(14:0/12:0)")))

## apply the function
add_edge_attributes(g, attributes)

michaelwitting/wormLipidPredictR documentation built on Dec. 20, 2024, 5:35 a.m.