foodingraph (version 0.1.0)

links_nodes_from_mat: Extracts links and nodes

Description

From an adjacency matrix, extracts two data.frames/tibbles

1. Links. columns : from, to, with, weight

2. Nodes. columns : name, title. name corresponds to the names used in 'from' and 'to'

Usage

links_nodes_from_mat(adjacency_matrix, legend, threshold = 0,
  abs_threshold = TRUE, filter_nodes = TRUE)

Arguments

adjacency_matrix

: a matrix of size n x n, each element being a number explaining the relationship e.g. coefficient, information between two variables given in the column and row names /!\ As this code is to draw undirected graphs, only the lower triangular part of adjacency matrix is used to extract the information.

legend

: a data frame of columns in order : 1) name, str : name of the node in the adjacency matrix, e.g. CRUDSAL_cat 2) title, str : name of the node, e.g. Raw vegetables 3) family, factor : (optional) the family the node belongs to, e.g. Vegetables

threshold

numeric) : a number defining the minimal threshold. If the weights are less than this threshold, they will be set to 0.

abs_threshold

(bool) : should the threshold keep negative values, e.g. if abs_threshold is set to TRUE, and threshold is set to 0.1, all weights between -0.1 and 0.1 will be set to 0

filter_nodes

(bool) : should the variables not in the adjacency matrix be displayed on the graph? Default is TRUE CAREFUL : if set to TRUE, be sure to have the same colors in the family legend of the graphs. A fixed palette can be set using the family_palette func.

Value

A list of two data frames : links and nodes.

Examples

# NOT RUN {
adj_matrix <- cor(iris[,-5])
legend <- data.frame(name = colnames(iris[,-5]),
                     title = colnames(iris[,-5]))
links_nodes_from_mat(adj_matrix, legend)
# }