plot_module {GWENA} | R Documentation

## 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,
      lower_weight_th = NULL,
      upper_weight_th = NULL,
      enrichment = 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,
      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.
`lower_weight_th, upper_weight_th` | decimal, weight threshold below or above which edges will be removed.
`enrichment` | list, representing a gost object.
`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.
`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)

[Package GWENA version 1.0.1 Index]