Plot Relationship Network

This function plots a relationship network that includes functional modules, modules, pathways, and molecules.

plot_relationship_network(
  object,
  include_functional_modules = TRUE,
  include_modules = TRUE,
  include_pathways = TRUE,
  include_molecules = TRUE,
  functional_module_color = "#F05C3BFF",
  module_color = "#46732EFF",
  pathway_color = "#197EC0FF",
  molecule_color = "#3B4992FF",
  functional_module_text = TRUE,
  module_text = TRUE,
  pathway_text = TRUE,
  molecule_text = FALSE,
  functional_module_text_size = 3,
  module_text_size = 3,
  pathway_text_size = 3,
  molecule_text_size = 3,
  circular_plot = FALSE,
  functional_module_arrange_position = TRUE,
  module_arrange_position = TRUE,
  pathway_arrange_position = TRUE,
  molecule_arrange_position = TRUE,
  functional_module_position_limits = c(0, 1),
  module_position_limits = c(0, 1),
  pathway_position_limits = c(0, 1),
  molecule_position_limits = c(0, 1)
)

Arguments

object

An object of class "functional_module".

include_functional_modules

Logical; include functional modules in the plot?

include_modules

Logical; include modules in the plot?

include_pathways

Logical; include pathways in the plot?

include_molecules

Logical; include molecules in the plot?

functional_module_color

Character; color for functional modules.

module_color

Character; color for modules.

pathway_color

Character; color for pathways.

molecule_color

Character; color for molecules.

functional_module_text

Logical; include functional module text labels?

module_text

Logical; include module text labels?

pathway_text

Logical; include pathway text labels?

molecule_text

Logical; include molecule text labels?

functional_module_text_size

Numeric; size of functional module text labels.

module_text_size

Numeric; size of module text labels.

pathway_text_size

Numeric; size of pathway text labels.

molecule_text_size

Numeric; size of molecule text labels.

circular_plot

Logical; make the plot circular?

functional_module_arrange_position

Logical; should the position of functional modules be arranged?

module_arrange_position

Logical; should the position of modules be arranged?

pathway_arrange_position

Logical; should the position of pathways be arranged?

molecule_arrange_position

Logical; should the position of molecules be arranged?

functional_module_position_limits

Numeric vector; limits for functional module positions.

module_position_limits

Numeric vector; limits for module positions.

pathway_position_limits

Numeric vector; limits for pathway positions.

molecule_position_limits

Numeric vector; limits for molecule positions.

Value

A ggplot object representing the relationship network.

Author

Xiaotao Shen shenxt1990@outlook.com