meMultiplex_communities.RdFor two `igraph` layers with shared nodes, the function finds `Infomap` communities of the constructed multiplex. Function interprets the first layer as correlation layer. The second layer, if weighted, should have only positive weights and can be interpreted as distance layer.
`Infomap` has to be locally installed for this function to work. Help with installation and alternative ways to run the `Infomap` algorithm are explained in 'Details'.
meMultiplex_communities( cor_layer, supplementary_layer, physical_nodes = FALSE, layer = 1, folder = "./meNet/", file_basename = "meNet_infomap", infomap_call = "infomap", cor_weighted = TRUE, supp_weighted = TRUE, cor_normalization_fun = max_normalization, supp_normalization_fun = neg_max_normalization, inter_cor_supp = NULL, inter_supp_cor = inter_cor_supp, infomap_seed = NULL, relaxation_rate = 0.15, delete_files = FALSE )
| cor_layer | Correlation layer of the multiplex as igraph object. |
|---|---|
| supplementary_layer | Supplementary layer of the multiples as igraph object. |
| physical_nodes | Should physical or state nodes be used for community structure nodes. Default to `FALSE`, i.e. to state nodes. |
| layer | The layer from which the community structure is obtained. Only used for state nodes. |
| folder | Folder in which the files will be saved. It is automatically created if not already present. Default value is `"./meNet/"`. |
| file_basename | Base name of the creates files. For different files, different suffix is added to the base name. Default value is `"meNet_infomap"`. |
| infomap_call | Path to the `Infomap` on user's system. Defaults to `"infomap"`. |
| cor_weighted | Whether the correlation layer is weighted. Passed to `meMultiplex`. Defaults to `TRUE`. |
| supp_weighted | Whether the supplementary layer is weighted. Passed to `meMultiplex`. Defaults to `TRUE`. |
| cor_normalization_fun | Normalization function for the correlation layer. Passed to `meMultiplex`. Defaults to `max_normalization`. |
| supp_normalization_fun | Normalization function for the supplementary layer. Passed to `meMultiplex`. Defaults to `neg_max_normalization`. |
| inter_cor_supp | Weight of the inter-layer edges. Passed to `meMultiplex`. Defaults to `NULL`. |
| inter_supp_cor | Weight of the inter-layer edges. Passed to `meMultiplex`. By default, the values is equal to `inter_cor_supp`. |
| infomap_seed | `seed` parameter in `Infomap` call. By default, no seed is set. |
| relaxation_rate | `multilayer-relax-rate` parameter in `Infomap` call. Default to `0.15`. |
| delete_files | Should created files be automatically deleted from the user's system. Default to `FALSE`. Changing the parameter to `TRUE` should be done with caution since it will allow the function to delete files from user's system. |
Data frame with two columns. The first column contains names of nodes and the second column contains corresponding `Infomap` community.
Function finds communities of nodes (CpGs) performing a sequence of three action. Firstly, `meMultiplex` function is called and the structure of multiplex if written to a file. The file is used in a call of to `Infomap` which performs the clustering of nodes. The clusters are saved to a file. In the end, function `read_infomap_communities` reads the community structure of the multiplex from the two files and returns a tidy data frame with nodes and their corresponding communities.
For multiplex reconstruction, parameters `cor_layer`, `supplementary_layer`, `cor_weighted`, `supp_weighted`, `cor_normalization_fun`, `supp_normalization_fun`, `inter_cor_supp` and `inter_supp_cor` are passed to the `meMultiplex` with `output_type` set to `"infomap"`.
`Infomap` is called from the command line using the path given in `infomap_call` with flags `-i multilayer -o clu`. If specified, `infomap_seed` is added as `--seed` flag and `relaxation-rate` is added as `--multilayer-relax-rate` flag. For help with the installation of the `Infomap` algorithm, visit `Infomap` website: https://www.mapequation.org/infomap/. If the installation fails, the output of the `meMultiplex` can be manually uploaded online on the `Infomap` website and the resulting '.clu` files can be used as input to `read_infomap_community` function. For futher details, refer to `Infomap` paper (De Domenico et al. 2015) .
To read multiplex communities, function `read_infomap_communities` is called with the location of two files from the previous steps. Parameters `physical_nodes` and `layer` are passed to the function.
In the first two steps of the function algorithm, files are created and saved in the `folder` using `file_basename`. These files are by-product of the function and can be deleted if the user doesn't want to examine their details. If `delete_files` is `TRUE`, these files will be automatically deleted from the user's system. If the folder contains only these files, it will also be deleted.
De Domenico M, Lancichinetti A, Arenas A, Rosvall M (2015). “Identifying modular flows on multilayer networks reveals highly overlapping organization in interconnected systems.” Physical Review X, 5(1), 011027.