inst/doc/introduction.R

In cograph: Analysis and Visualization of Complex Networks

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 6,
  fig.height = 6,
  fig.dpi = 50,
  dpi = 50
)

## ----setup--------------------------------------------------------------------
library(cograph)

## ----matrix-input-------------------------------------------------------------
# Create a simple adjacency matrix
adj <- matrix(c(
  0, 1, 1, 0, 0,
  1, 0, 1, 1, 0,
  1, 1, 0, 1, 1,
  0, 1, 1, 0, 1,
  0, 0, 1, 1, 0
), nrow = 5, byrow = TRUE)

# Add labels
rownames(adj) <- colnames(adj) <- c("A", "B", "C", "D", "E")

# Create and render
cograph(adj)

## ----edgelist-input-----------------------------------------------------------
edges <- data.frame(
  from = c("Alice", "Alice", "Bob", "Carol"),
  to = c("Bob", "Carol", "Carol", "Dave"),
  weight = c(1, 2, 1, 3)
)

cograph(edges)

## ----layout-circle------------------------------------------------------------
cograph(adj, layout = "circle")

## ----layout-spring------------------------------------------------------------
cograph(adj, layout = "spring", seed = 42)

## ----layout-groups------------------------------------------------------------
groups <- c(1, 1, 2, 2, 2)
cograph(adj) |>
  sn_layout("groups", groups = groups)

## ----node-customization-------------------------------------------------------
cograph(adj) |>
  sn_nodes(
    size = 0.08,
    shape = "circle",
    fill = "steelblue",
    border_color = "navy",
    border_width = 2
  )

## ----node-per-node------------------------------------------------------------
cograph(adj) |>
  sn_nodes(
    size = c(0.05, 0.06, 0.08, 0.06, 0.05),
    fill = c("red", "orange", "yellow", "green", "blue")
  )

## ----node-shapes--------------------------------------------------------------
cograph(adj) |>
  sn_nodes(
    shape = c("circle", "square", "triangle", "diamond", "star")
  )

## ----edge-basic---------------------------------------------------------------
cograph(adj) |>
  sn_edges(
    width = 2,
    color = "gray40",
    alpha = 0.7
  )

## ----edge-weighted------------------------------------------------------------
# Create weighted adjacency matrix
weighted <- matrix(c(
  0, 0.8, -0.5, 0, 0,
  0.8, 0, 0.3, -0.7, 0,
  -0.5, 0.3, 0, 0.6, -0.4,
  0, -0.7, 0.6, 0, 0.9,
  0, 0, -0.4, 0.9, 0
), nrow = 5, byrow = TRUE)

cograph(weighted) |>
  sn_edges(
    width = "weight",
    color = "weight",
    positive_color = "darkgreen",
    negative_color = "darkred"
  )

## ----edge-directed------------------------------------------------------------
# Create directed network
dir_adj <- matrix(c(
  0, 1, 1, 0, 0,
  0, 0, 1, 1, 0,
  0, 0, 0, 1, 1,
  0, 0, 0, 0, 1,
  0, 0, 0, 0, 0
), nrow = 5, byrow = TRUE)

cograph(dir_adj, directed = TRUE) |>
  sn_edges(
    curvature = 0.1,
    arrow_size = 0.015
  )

## ----theme-classic------------------------------------------------------------
cograph(adj) |> sn_theme("classic")

## ----theme-dark---------------------------------------------------------------
cograph(adj) |> sn_theme("dark")

## ----theme-minimal------------------------------------------------------------
cograph(adj) |> sn_theme("minimal")

## ----theme-colorblind---------------------------------------------------------
cograph(adj) |> sn_theme("colorblind")

## ----ggplot-conversion--------------------------------------------------------
library(ggplot2)

p <- cograph(adj) |>
  sn_nodes(fill = "coral") |>
  sn_ggplot()

p +
  labs(
    title = "My Network",
    subtitle = "Created with cograph"
  ) +
  theme(plot.title = element_text(hjust = 0.5))

## ----complete-example---------------------------------------------------------
# Social network example
social <- matrix(c(
  0, 1, 1, 0, 0, 0,
  1, 0, 1, 1, 0, 0,
  1, 1, 0, 1, 1, 0,
  0, 1, 1, 0, 1, 1,
  0, 0, 1, 1, 0, 1,
  0, 0, 0, 1, 1, 0
), nrow = 6, byrow = TRUE)

rownames(social) <- colnames(social) <-
  c("Alice", "Bob", "Carol", "Dave", "Eve", "Frank")

groups <- c("Team A", "Team A", "Team A", "Team B", "Team B", "Team B")

social |>
  cograph() |>
  sn_layout("groups", groups = groups) |>
  sn_nodes(
    size = 0.06,
    fill = ifelse(groups == "Team A", "#E69F00", "#56B4E9"),
    border_width = 2
  ) |>
  sn_edges(width = 1.5, alpha = 0.6) |>
  sn_theme("minimal") |>
  sn_render(title = "Social Network")

## ----saving, eval=FALSE-------------------------------------------------------
# net <- cograph(adj) |>
#   sn_nodes(fill = "steelblue") |>
#   sn_theme("minimal")
# 
# # Save as PDF
# sn_save(net, "network.pdf", width = 8, height = 8)
# 
# # Save as PNG
# sn_save(net, "network.png", width = 8, height = 8, dpi = 300)
# 
# # Save as SVG
# sn_save(net, "network.svg", width = 8, height = 8)