add_vertex_attributes: Add vertex attributes to 'igraph' object

In michaelwitting/wormLipidPredictR: Lipid reaction prediction based on WormJam

Add vertex attributes to igraph object

Description

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

The attributes object is a data.frame.

The data.frame contains the columns col_vertex, a character vector of length 1, specifying the vertices and the vertex attributes weights in the remaining columns. The attributes will be stored in the respective slots with same names as the colnames of attributes for each vertex of the returned igraph object.

Usage

add_vertex_attributes(g, attributes, col_vertex = colnames(attributes)[1])

Arguments

g	igraph object
attributes	data.frame containing vertex attribute information
col_vertex	chararacter of length 1, specifying the column containing vertices in attributes of type data.frame

Details

col_vertex has to be adjusted such that it specifies the vertices. The character of length 1 will specify the column containing the 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_df <- data.frame(
   name = c("CoA(12:0)", "CoA(14:0)", "CoA(16:0)", "DG(12:0/12:0/0:0)",
       "DG(12:0/14:0/0:0)", "DG(12:0/16:0/0:0)", "DG(14:0/12:0/0:0)",
       "DG(14:0/14:0/0:0)", "DG(14:0/16:0/0:0)", "DG(16:0/12:0/0:0)",
       "DG(16:0/14:0/0:0)", "DG(16:0/16:0/0:0)", "FA(12:0)", "FA(14:0)",
       "FA(16:0)", "PA(12:0/0:0)", "PA(12:0/12:0)", "PA(12:0/14:0)",
       "PA(12:0/16:0)", "PA(14:0/0:0)", "PA(14:0/12:0)", "PA(14:0/14:0)", 
       "PA(14:0/16:0)", "PA(16:0/0:0)", "PA(16:0/12:0)", "PA(16:0/14:0)",
       "PA(16:0/16:0)"),
   logFC_cond1 = c(-5.08,  0.75,  5.43, -0.62,  2.35, 1.39, 2.91,  0.26, 
       -4.14,  0.19,  6.18, 0.78, -1.81,  4.66, -0.10,  2.84, -0.81,
       -0.81, -0.32,  0.17,  2.25, -1.94,  0.80, 4.21,  0.20, -3.29, 
       -0.11),
   logFC_cond2 = c(-2.73,  6.14,  1.98,  0.09,  1.57,  1.77,  3.08,  4.04,
       -3.01, 1.22, -4.25, 0.39, 0.53, 3.30, 7.10, 2.81, -0.99, -0.09,
       -8.25, 4.94, -3.54, -7.74, -1.98, 0.73,  2.36,  2.53, -0.62))

## apply the function
add_vertex_attributes(g = g, attributes = attributes_df, col_vertex = "name")

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