plot_module: Plot co-expression network

In Kumquatum/GWENA: Pipeline for augmented co-expression analysis

Plot co-expression network

Description

Display a graph representing the co-expression network and different informations like hubs, enrichments

Usage

plot_module(
  graph_module,
  hubs = NULL,
  groups = NULL,
  lower_weight_th = NULL,
  upper_weight_th = NULL,
  title = "Module",
  degree_node_scaling = TRUE,
  node_scaling_min = 1,
  edge_scaling_min = 0.2,
  node_scaling_max = 6,
  edge_scaling_max = 1,
  nb_row_legend = 6,
  layout = "auto",
  zoom = 1,
  vertex.label.cex = 0.7,
  vertex.label.color = "gray20",
  vertex.label.family = "Helvetica",
  edge.color = "gray70",
  vertex.frame.color = "white",
  vertex.color = "gray60",
  vertex.label.dist = 1,
  legend_cex = 0.8,
  groups_palette = NULL,
  window_x_min = -1,
  window_x_max = 1,
  window_y_min = -1,
  window_y_max = 1,
  legend = TRUE,
  ...
)

Arguments

graph_module	igraph object, module to plot.
hubs	character vector or numeric vector with names, optionnal, vector of gene names or vector of numeric values named with gene names.
groups	matrix or data.frame, a two cols table with the gene id in the first one, and the group assignation in the second one.
lower_weight_th, upper_weight_th	decimal, weight threshold above lower_weight_th or below upper_weight_th which edges will be removed.
title	string, main title that will be displayed on the plot.
degree_node_scaling	boolean, indicates if node size should represent the degree of this node.
node_scaling_min, node_scaling_max	integer, if degree_node_scaling is TRUE, it is the min/max size of the node, else it is the exact size of all node.
edge_scaling_min, edge_scaling_max	integer, min/max width of the edge
nb_row_legend	integer, number of levels in the legend.
layout	numeric matrix or function or string, numeric matrix for nodes coordinates, or function for layout, or name of a layout function available in igraph. Default "auto" will choose the best layout depending on the graph. For more information, see igraph.plotting.
zoom	integer, scaling factor by which it's possible to have compact graph (< 1) or larger graph (> 1) display.
vertex.label.cex, legend_cex	float, font size for vertex labels. It is interpreted as a multiplication factor of some device-dependent base font size. If 0, no labels displayed.
vertex.label.color, edge.color, vertex.frame.color, vertex.color	character and/or integer vector , color of the labels. It may either contain integer values, named colors or RGB specified colors with three or four bytes. All strings starting with ‘#’ are assumed to be RGB color specifications. It is possible to mix named color and RGB colors.
vertex.label.family	character, font family to be used for vertex labels.
vertex.label.dist	integer, distance of the label from the center of the vertex. If it is 0 then the label is centered on the vertex. If it is 1 then the label is displayed beside the vertex.
groups_palette	character and/or integer vector, vertices group palette of colors for the groups specified. It may either contain integer values, named colors or RGB specified colors with three or four bytes. All strings starting with ‘#’ are assumed to be RGB color specifications. It is possible to mix named color and RGB colors.
window_x_min	decimal, value for the bottom limit of the window.
window_x_max	decimal, value for the top limit of the window.
window_y_min	decimal, value for the left limit of the window.
window_y_max	decimal, value for the right limit of the window.
legend	boolean, indicates if the legend should be plotted.
...	any other parameter compatible with the plot.igraph function.

Details

Take care of you intend to compare modules' graphs, the same size of node will not correspond to the same values because of the scaling.

Value

matrix, layout of the graph as a two column matrix (x, y)

Examples

mat <- matrix(runif(40*40), 40)
g <- build_graph_from_sq_mat(mat)
plot_module(g, lower_weight_th = -0.5, upper_weight_th = 0.5)

Kumquatum/GWENA documentation built on July 7, 2023, 3:41 p.m.