The position of the nodes is based on the similarity between them.

Plot how similar are the data

Usage

plot_data(x, top)

plot_similarity(pd)

Arguments

x: Matrix with the similarities.
top: a number between 0 and 1 to select the edges relating the elements of the matrix.
pd: The plot data from plot_data() function.

Value

A list with two elements:

nodes: The position and name of the nodes
edges: The information about the selected edges

A ggplot object

Examples

if (require("org.Hs.eg.db") & require("reactome.db")) {
  # Extract the paths of all genes of org.Hs.eg.db from KEGG
  # (last update in data of June 31st 2011)
  genes.kegg <- as.list(org.Hs.egPATH)
  # Extracts the paths of all genes of org.Hs.eg.db from reactome
  genes.react <- as.list(reactomeEXTID2PATHID)

  sim <- mgeneSim(c("81", "18", "10"), genes.react)
  pd <- plot_data(sim, top = 0.25)
  if (requireNamespace("ggplot2", quietly = TRUE)){
    plot_similarity(pd)
  }
}