Plot a ggig

Plot a ggig

# S3 method for class 'ggig'
plot(
  x,
  coors = NULL,
  ...,
  labels_num = NULL,
  vertex_size_range = NULL,
  edge_width_range = NULL,
  plot_module = FALSE,
  mark_module = FALSE,
  mark_color = NULL,
  mark_alpha = 0.3,
  module_label = FALSE,
  module_label_cex = 2,
  module_label_color = "black",
  module_label_just = c(0.5, 0.5),
  legend_number = FALSE,
  legend = TRUE,
  legend_cex = 1,
  legend_position = c(left_leg_x = -2, left_leg_y = 1, right_leg_x = 1.2, right_leg_y =
    1),
  group_legend_title = NULL,
  group_legend_order = NULL,
  color_legend = TRUE,
  color_legend_order = NULL,
  size_legend = FALSE,
  size_legend_title = "Node Size",
  edge_legend = TRUE,
  edge_legend_title = "Edge type",
  edge_legend_order = NULL,
  width_legend = FALSE,
  width_legend_title = "Edge width",
  lty_legend = FALSE,
  lty_legend_title = "Edge class",
  lty_legend_order = NULL,
  params_list = NULL,
  seed = 1234
)

Arguments

x: ggig object
coors: the coordinates you saved
...: additional parameters for igraph.plotting
labels_num: show how many labels, >1 indicates number, <1 indicates fraction, "all" indicates all.
vertex_size_range: the vertex size range, e.g. c(1,10)
edge_width_range: the edge width range, e.g. c(1,10)
plot_module: logical, plot module?
mark_module: logical, mark the modules?
mark_color: mark color
mark_alpha: mark fill alpha, default 0.3
module_label: show module label?
module_label_cex: module label cex
module_label_color: module label color
module_label_just: module label just, default c(0.5,0.5)
legend_number: legend with numbers
legend: all legends
legend_cex: character expansion factor relative to current par("cex"), default: 1
legend_position: legend_position, default: c(left_leg_x=-1.9,left_leg_y=1,right_leg_x=1.2,right_leg_y=1)
group_legend_title: group_legend_title, length must same to the numbers of v_group
group_legend_order: group_legend_order vector
color_legend: logical
color_legend_order: color_legend_order vector
size_legend: logical
size_legend_title: size_legend_title
edge_legend: logical
edge_legend_title: edge_legend_title
edge_legend_order: edge_legend_order vector, e.g. c("positive","negative")
width_legend: logical
width_legend_title: width_legend_title
lty_legend: logical
lty_legend_title: lty_legend_title
lty_legend_order: lty_legend_order
params_list: a list of parameters, e.g. list(edge_legend = TRUE, lty_legend = FALSE), when the parameter is duplicated, the format argument will be used rather than the argument in params_list.
seed: random seed, default:1234, make sure each plot is the same.

Value

ggplot

Arguments

Value

See also