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+++ b/R/combine_layers.R
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+#' Combine layers
+#'
+#' Return a merged graph from two graph layers.
+#'
+#' @param graph1 an igraph object or list of igraph (\code{list.igraph}).
+#' @param graph2 an igraph object or list of igraph (\code{list.igraph}) with 
+#'                the same length as \code{graph1}.
+#' @param interaction.df (optional) a 2 colomns data.frame (from, to) 
+#' describing the edges between vertices from both graphs.
+#' 
+#' @details
+#' If \code{graph2} is a single graph, it will be merged to each element of 
+#' \code{graph1} (\code{igraph} or \code{list.igraph}).
+#' 
+#' If \code{graph2} is a list of graph (\code{list.igraph}), each element of 
+#' \code{graph1} and each element of \code{graph2} are merged in pairs.
+#' 
+#' Optionally, \code{interaction.df} should be provide if any vertex are shared 
+#' between graphs. It can also be used to extend the first graph.
+#' 
+#' In both scenarios, vertex attributes are kept. If a vertex attribute is 
+#' missing from graph1 or graph2, NULL value is added.
+#' Otherwise, if there is an overlap between attribute values for the same 
+#' vertex, attribute from graph2 is dropped.
+#' 
+#' @return 
+#' a merged graph with both vertex attributes from graph1 and graph2.
+#'
+#' @examples
+#' # with single graphs
+#' graph1 <- igraph::graph_from_data_frame(list(from = c('A', 'B'),
+#'                                              to = c('B', 'C')),
+#'                                         directed = FALSE)
+#' graph2 <- igraph::graph_from_data_frame(list(from = c(1), 
+#'                                              to = c(2)),
+#'                                         directed = FALSE)
+#' res <- combine_layers(graph1 = graph1,
+#'                       graph2 = graph2)
+#' 
+#' # with list of graphs
+#' graph1.list <- list(graph1, graph1)
+#' graph2.list <- list(graph2, graph2)
+#' class(graph1.list) <- class(graph2.list) <- 'list.igraph'
+#' 
+#' res <- combine_layers(graph1 = graph1.list, 
+#'                       graph2 = graph2)
+#' res <- combine_layers(graph1 = graph1.list, 
+#'                       graph2 = graph2.list)
+#' 
+#' # with interaction dataframe
+#' interaction.df1 <- as.data.frame(list(from = c('C', 'B'), to = c(1, 2)))
+#' res <- combine_layers(graph1 = graph1.list, 
+#'                       graph2 = graph2, 
+#'                       interaction.df = interaction.df1)
+#' 
+#' 
+#' @importFrom purrr is_empty map reduce map2
+#' @importFrom igraph induced_subgraph
+#' @importFrom igraph set_vertex_attr
+#' @importFrom igraph adjacent_vertices
+#' @importFrom igraph graph_from_data_frame
+#' @importFrom igraph vcount
+#' @importFrom igraph V
+#' @importFrom igraph as.undirected
+
+#' @export
+combine_layers <- function(graph1, 
+                           graph2 = NULL, 
+                           interaction.df = NULL) {
+    
+    # check graph1
+    if (!is(graph1, "igraph") & !is(graph1, "list.igraph")) {
+        stop("graph1 must be an igraph or list.igraph object")
+    }
+    if (is(graph1, "list.igraph")) {
+        if (is.null(names(graph1))) {
+            names(graph1) <- seq_along(graph1)
+        }
+    }
+    
+    if (!is(graph2, "igraph") & !is(graph2, "list.igraph") & !is.null(graph2)) {
+        stop("graph2 must be an igraph or list.igraph object or NULL")
+    }
+    if (!is.null(interaction.df)) {
+        interaction.df <- check_db(interaction.df)
+        
+        if (!is(interaction.df, "igraph")) {
+            interaction.df <- interaction.df %>%
+                dplyr::select(c("from", "to"))
+            interaction.graph <- igraph::graph_from_data_frame(interaction.df, 
+                                                               directed = FALSE)
+        } else {
+            interaction.graph <- igraph::as.undirected(interaction.df)
+        }
+    }
+    
+    # case1: graph2 = NULL, interaction.df = NULL
+    if (is.null(graph2) & is.null(interaction.df)) {
+        merged.res <- graph1
+    }
+    
+    # case2: graph1 and graph2 are single graph (+ interaction.df)
+    if (is(graph1, "igraph") & is(graph2, "igraph")) {
+        merged.res <- merge_graphs(graph1, graph2)
+        if (!is.null(interaction.df)) {
+            # interaction.graph can be not found, df can be NULL
+            interaction.graph.induced <- igraph::induced_subgraph(
+                graph = interaction.graph, 
+                vids = intersect(igraph::V(interaction.graph)$name, 
+                                 igraph::V(merged.res)$name))
+            merged.res <- merge_graphs(merged.res, 
+                                       interaction.graph.induced)
+        }
+        
+        # case3: graph1 is a list and graph2 is a single graph 
+        # (+ interaction.df)
+    } else if (is(graph1, "list.igraph") & is(graph2, "igraph")) {
+        merged.res <- purrr::map(graph1, ~{
+            merge_graphs(.x, graph2)
+        })
+        names(merged.res) <- names(graph1)
+        if (!is.null(interaction.df)) {
+            # interaction.graph can be not found, df can be NULL 
+            # merged.res <- list() # already defined
+            for (i in names(merged.res)) {
+                interaction.graph.induced <- igraph::induced_subgraph(
+                    graph = interaction.graph, 
+                    vids = intersect(igraph::V(interaction.graph)$name,
+                                     igraph::V(merged.res[[i]])$name))
+                merged.res[[i]] <- merge_graphs(merged.res[[i]], 
+                                                interaction.graph.induced)
+            }
+        }
+        
+        # case4: graph1 and graph2 are list of graph (+ interaction.df)
+    } else if (is(graph1, "list.igraph") & is(graph2, "list.igraph")) {
+        if (length(graph1) != length(graph2)) {
+            stop("graph1 and graph2 must have the same length")
+        }
+        if (!is.null(names(graph1)) & !is.null(names(graph2))) {
+            # graph1 and graph2 have names same length 
+            # so reciprocal is TRUE they don't have the same names
+            if (!all(names(graph1) %in% names(graph2))) {
+                stop("graph1 and graph2 must have the same names")
+            } else {
+                merged.res <- purrr::map2(graph1, graph2[names(graph1)], ~{
+                    merge_graphs(.x, .y)
+                })
+            }
+        } else {
+            # no names, don't care about the order
+            merged.res <- purrr::map2(graph1, graph2, ~{
+                merge_graphs(.x, .y)
+            })
+            names(merged.res) <- names(graph1)
+        }
+        if (!is.null(interaction.df)) {
+            # interaction.graph can be not found, df can be NULL
+            for (i in names(merged.res)) {
+                interaction.graph.induced <- igraph::induced_subgraph(
+                    graph = interaction.graph, 
+                    vids = intersect(igraph::V(interaction.graph)$name,
+                                     igraph::V(merged.res[[i]])$name))
+                merged.res[[i]] <- merge_graphs(merged.res[[i]], 
+                                                interaction.graph.induced)
+            }
+        }
+        
+        # case5: inverse of case3 -> error
+    } else if (is(graph1, "igraph") & is(graph2, "list.igraph")) {
+        stop("graph1 and graph2 must have the same length")
+        
+        # case6: graph1 and interaction.df
+    } else if (is(graph1, "igraph") & 
+               is.null(graph2) & 
+               !is.null(interaction.df)) {
+        interaction.df.sub <- interaction.df %>%
+            dplyr::filter(.$from %in% igraph::V(graph1)$name | 
+                              .$to %in% igraph::V(graph1)$name)
+        interaction.graph <- igraph::graph_from_data_frame(interaction.df.sub, 
+                                                           directed = FALSE)
+        merged.res <- merge_graphs(graph1, interaction.graph)
+        
+        # case7: graph1 list and interaction.df
+    } else if (is(graph1, "list.igraph") & 
+               is.null(graph2) & 
+               !is.null(interaction.df)) {
+        merged.res <- list()
+        for (i in names(graph1)) {
+            interaction.df.sub <- interaction.df %>%
+                dplyr::filter(.$from %in% igraph::V(graph1[[i]])$name | 
+                                  .$to %in% igraph::V(graph1[[i]])$name)
+            interaction.graph <- igraph::graph_from_data_frame(
+                interaction.df.sub, 
+                directed = FALSE)
+            merged.res[[i]] <- merge_graphs(graph1[[i]], interaction.graph)
+        }
+    }
+    
+    if (is(merged.res, "list")) {
+        class(merged.res) <- c("list.igraph", "list.merged.igraph")
+    }
+    return(merged.res)
+}
+
+
+#' @importFrom igraph vertex_attr 
+#' @importFrom igraph union 
+#' @importFrom igraph delete_vertex_attr 
+#' @importFrom igraph set_vertex_attr 
+#' @importFrom igraph vcount
+merge_graphs <- function(graph1, 
+                         graph2) {
+    # shared attr except 'name'
+    shared_attr <- intersect(names(igraph::vertex_attr(graph1)), 
+                             names(igraph::vertex_attr(graph2)))
+    shared_attr <- shared_attr[!(shared_attr == "name")]
+    
+    merged_graphs <- igraph::union(graph1, graph2)
+    # vertex_attr(merged_graphs) %>% as.data.frame()
+    merged_attr <- igraph::vertex_attr(merged_graphs)
+    for (sa in shared_attr) {
+        merged_attr[[sa]] <- vector(length = igraph::vcount(merged_graphs))
+        for (i in seq_along(merged_attr[[sa]])) {
+            # if !is.na _1, return _1 else return _2
+            merged_attr[[sa]][i] <- 
+                ifelse(!is.na(merged_attr[[paste0(sa, "_1")]][i]), 
+                       merged_attr[[paste0(sa, "_1")]][i], 
+                       merged_attr[[paste0(sa, "_2")]][i])
+        }
+        merged_graphs <- delete_vertex_attr(graph = merged_graphs, 
+                                            name = paste0(sa, "_1"))
+        merged_graphs <- delete_vertex_attr(graph = merged_graphs, 
+                                            name = paste0(sa, "_2"))
+        merged_graphs <- set_vertex_attr(graph = merged_graphs, 
+                                         name = sa, value = merged_attr[[sa]])
+    }
+    class(merged_graphs) <- c("merged.igraph", "igraph")
+    return(merged_graphs)
+}