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,
      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)

[Package GWENA version 1.4.0 Index]