links_nodes_from_mat: Extracts links and nodes
In foodingraph: Food Network Inference and Visualization

Description Usage Arguments Value Examples

View source: R/links_nodes_from_mat.R

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

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

1 2	links_nodes_from_mat(adjacency_matrix, legend, threshold = 0, abs_threshold = TRUE, filter_nodes = TRUE)

`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.

A list of two data frames : links and nodes.

adj_matrix <- cor(iris[,-5])
legend <- data.frame(name = colnames(iris[,-5]),
                     title = colnames(iris[,-5]))
links_nodes_from_mat(adj_matrix, legend)