meMultiplex_communities: Multiplex community structure
In ivabudimir/meNet: Correlation-based network analysis of methylation data

Description Usage Arguments Details Value References

View source: R/meMultiplex_communities.R

For 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.

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 \insertCiteinfomapmeNet.

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.

Data frame with two columns. The first column contains names of nodes and the second column contains corresponding 'Infomap' community.

\insertAllCited

ivabudimir/meNet documentation built on Dec. 20, 2021, 8:03 p.m.