plot_multiplex.RdPlots a multiplex network from two `igraph` layers. It is a corresponding plotting function for `meMultiplex` function which plots two layers next to each other preserving the location of shared nodes. As in `meMultiplex`, the first layer can contain negative edge weights while the second layer must have only non-negative weights.
plot_multiplex( first_layer, second_layer, layout_layer = "first", module_df = NULL, first_weighted = TRUE, second_weighted = TRUE, first_normalization_fun = .max_normalization, second_normalization_fun = .neg_max_normalization, include_negative = TRUE, node_sort_fun = .coord_sort, layout_fun = igraph::layout_with_fr, layout_weighted = FALSE, layout_weight_transformation_fun = .max_normalization, main_title = NULL, first_title = "Correlation", second_title = "CpG island", node_col = "black", node_size = 2, pos_edge_col = "grey70", neg_edge_col = "blue", plot_module = FALSE, module_border_col = "black", module_border_expand = 10, plot_layout_graph = FALSE )
| first_layer | The first layer of the multiplex as `igraph` object. |
|---|---|
| second_layer | The second layer of the multiplex as `igraph` object. |
| layout_layer | Defines the plotting method used to determines the layout of nodes. Can take values `"first"`, `"second"`, `"module"`, `"aggregated"` or `"coord"`. See 'Details'. |
| module_df | Data frame with community structure. The first column contains names of nodes and the second column contains corresponding community. It is mandatory parameter if `layout_layer="module"` or `plot_module=TRUE`. |
| first_weighted | Whether the first layer is weighted. If `FALSE`, all weights are set to `1`. Default to `TRUE`. |
| second_weighted | Whether the second layer is weighted. If `FALSE`, all weights are set to `1`. Default to `TRUE`. |
| first_normalization_fun | Normalization function applied on the weights of the first layer, if the layer is weighted. If `NULL`, no normalization is applied. Defaults to `max_normalization`. |
| second_normalization_fun | Normalization function applied on the weights of the second layer, if the layer is weighted. If `NULL`, no normalization is applied. Defaults to `neg_max_normalization`. |
| node_sort_fun | Sort function used on the nodes of the network. Default to `.coord_sort`, which sorts CpGs based on their genomic location. |
| layout_fun | Algorithm for the layout of the nodes used on the layout graph. In choosing of the function, attention should be paid whether weights of the layout graph represent "strength" or "cost". Default to `igraph::layout_with_fr`. |
| layout_weighted | Whether the edge weights of the layout graph are used by `layout_fun` to determine the layout of nodes. Default to `FALSE`. |
| layout_weight_transformation_fun | Normalization function applied on the weights of the layout graph, if the graph is weighted. If `NULL`, no normalization is applied. Defaults to `max_normalization`. |
| main_title | Main title of the plot. By default, there is no main title. |
| first_title | Title of the first subplot with the first layer of multiplex. Default value is `"Correlation"`. |
| second_title | Title of the second subplot with the second layer of multiplex. Default value is `"CpG island"`. |
| node_col | Color of the nodes. Color name if all nodes have the same color or data frame with node names in the first column and corresponding color in the second column. If some nodes are missing from the given data frame, their color is set to `"black"`. Defaults value of `node_col` is `"black"`. |
| node_size | Size of the nodes. Defaults to `2`. |
| pos_edge_col | Color of positive edges. Default value is `"grey70"`. |
| neg_edge_col | Color of negative edges. Default value is `"blue"`. |
| plot_module | Whether to plot the border around the communities defined in `module_df`. Defaults to `FALSE`. |
| module_border_col | Color of the border around the communities. Passed to `plot.igraph` as `mark.border` parameter. Defaults to `"black"`. |
| module_border_expand | Size of the border around the communities. Passed to `plot.igraph` as `mark.expand` parameter. Defaults to `10`. |
| plot_layout_graph | Whether to add a plot of layout graph. If `TRUE`, third plot is added to the right of the multiplex with the same layout of nodes and with edges from the layout graph. Default to `FALSE`. |
A vector of removed nodes.
Plots two-layer multiplex from two `igraph` layers. Layers are plotted next to each other with the same layout of nodes. Plotted edges represent edges found in a certain layer of multiplex. Parameters `main_title`, `first_title`, `second_title`, `node_col`, `node_size`, `pos_edge_col` and `neg_edge_col` help in customization of the plot.
Nodes which are isolated in both layers are removed from the multiplex. Nodes which are found only in one layer are added to the other layer as isolated nodes. This equalizes the set of nodes between two layers.
If `module_df` is given, borders can be plotted around the communities of nodes setting `plot_module` to `TRUE`. If the same node belong to multiple communities, only the first membership will be used in plotting. For customization, parameters `module_border_col` and `module_border_expand` can be used.
To determine the layout of nodes, new layout graph is constructed and used in the `layout_fun`. The nodes of the layout graph are the same as in the first and the second layer. If `layout_weighted`, the weight of edges are used by `layout_fun`. There are several option for the construction of the layout graph, depending on the value of `layout_layer`. If `layout_layer` has value
`"first"`layout graph is the first layer with removed negative edges;
`"second"`Layout graph is the second layer.
`"module"`Layout graph is constructed from `module_df`. In layout graph edges exist between nodes which are found in the same community. Weight of an edge is the number of communities in which a selected pair of nodes is found. Weight can be larger than `1` only if the same node can be a member of multiple communities in `module_df`.
`"aggregated"`Layout graph is obtained aggregating the first and the second layer. Weight of an edge in layout graph is the sum of weights of the same edge in the first and the second layer.
`"coord"`Layout graph is disconnected graph with no edges. This only makes sense if `layout_fun` uses circular layout since then nodes will be ordered by `node_sort_fun`.
Structure of the layout graph can be plotted as third layer setting `plot_layout_graph` to `TRUE`. It if not advisable to use this in the final plot, but this feature can be useful to find the appropriate `layout_fun`.
If layers are weighted, function searches for the edge attributes with names`"Cor"` and `"Dist"`. If the attribute doesn't exist, it takes the first edge attribute instead. The function handles weight of the first layer as correlations and weights of the second layer as distances. Function checks if all edge weights of `second_layer` are positive.