c_net_plot: Plot a metanet

In MetaNet: Network Analysis for Omics Data

Plot a metanet

Description

Plot a metanet

Usage

c_net_plot(
  go,
  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),
  pie_value = NULL,
  pie_color = NULL,
  legend = TRUE,
  legend_number = FALSE,
  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,
  module_legend = FALSE,
  module_legend_title = "Module",
  module_legend_order = NULL,
  pie_legend = FALSE,
  pie_legend_title = "Pie part",
  pie_legend_order = NULL,
  label_cex = 1,
  arrow_size_cex = 1,
  arrow_width_cex = 1,
  params_list = NULL,
  rescale = FALSE,
  seed = 1234
)

Arguments

go	an igraph or metanet 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)
pie_value	a dataframe using to plot pie (with rowname or a "name" column)
pie_color	color vector
legend	all legends
legend_number	legend with numbers
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
module_legend	logical
module_legend_title	module_legend_title
module_legend_order	module_legend_order
pie_legend	logical
pie_legend_title	pie_legend_title
pie_legend_order	pie_legend_order
label_cex	label cex, default 1, relative to the vertex size
arrow_size_cex	arrow size cex, default 1, relative to the vertex size
arrow_width_cex	arrow width cex, default 1, relative to the vertex size
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.
rescale	Logical constant, whether to rescale the coordinates to the (-1,1).
seed	random seed, default:1234, make sure each plot is the same.

Value

a network plot

See Also

Other plot: as.ggig(), input_cytoscape(), input_gephi(), netD3plot(), olympic_rings_net(), plot.ggig(), twocol_edgelist(), venn_net()

Examples

data("c_net")
c_net_plot(co_net)
c_net_plot(co_net2)
c_net_plot(multi1)

MetaNet documentation built on June 26, 2025, 5:07 p.m.