add directed params for network

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ggcor
 Type: Package
 Title: Extended tools for correlation analysis and visualization
-Version: 0.9.4.2
+Version: 0.9.4.3
 Authors@R: c(
     person("Houyun", "Huang", email = "[email protected]", role = c("aut", "cre")),
     person("Lei", "Zhou", email = "[email protected]", role = "aut"),

NAMESPACE

@@ -290,6 +290,7 @@ importFrom(grid,unit)
 importFrom(igraph,as.igraph)
 importFrom(igraph,as_data_frame)
 importFrom(igraph,graph_from_data_frame)
+importFrom(igraph,is.directed)
 importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,map_chr)

R/as-cor-network.R

@@ -1,6 +1,7 @@
 #' Coerce to a cor_network object
 #' @description Functions to coerce a object to cor_network if possible.
 #' @param x any \code{R} object.
+#' @param directed 	logical value, whether or not to create a directed graph.
 #' @param simplify logical value (defaults to TRUE) indicating whether to
 #'     delete nodes without edge connections.
 #' @param weight NULL (default) or name of column in edges which will be renamed
@@ -27,6 +28,7 @@ as_cor_network <- function(x, ...) {
 #' @export
 #' @method as_cor_network cor_tbl
 as_cor_network.cor_tbl <- function(x,
+                                   directed = FALSE,
                                    simplify = TRUE,
                                    weight = NULL,
                                    r.thres = 0.6,
@@ -80,57 +82,60 @@ as_cor_network.cor_tbl <- function(x,
     edges <- dplyr::rename(edges, weight = !!weight)
   }
 
-  structure(.Data = list(nodes = nodes,
-                         edges  = edges), class = "cor_network")
+  structure(.Data = list(nodes = nodes, edges  = edges),
+            directed = directed, class = "cor_network")
 }
 
 #' @rdname  as_cor_network
 #' @export
 #' @method as_cor_network mantel_tbl
-as_cor_network.mantel_tbl <- function(x, ...) {
-  as_cor_network(as_cor_tbl(x), ...)
+as_cor_network.mantel_tbl <- function(x, directed = FALSE, ...) {
+  as_cor_network(as_cor_tbl(x), directed = directed, ...)
 }
 
 #' @rdname  as_cor_network
 #' @export
 #' @method as_cor_network matrix
-as_cor_network.matrix <- function(x, ...) {
-  cor_network(corr = x, ..., val.type = "list")
+as_cor_network.matrix <- function(x, directed = FALSE, ...) {
+  cor_network(corr = x, directed = directed, ..., val.type = "list")
 }
 #' @rdname  as_cor_network
 #' @export
 #' @method as_cor_network data.frame
-as_cor_network.data.frame <- function(x, ...) {
-  cor_network(corr = x, ..., val.type = "list")
+as_cor_network.data.frame <- function(x, directed = FALSE, ...) {
+  cor_network(corr = x, directed = directed, ..., val.type = "list")
 }
 
 #' @rdname  as_cor_network
 #' @export
 #' @method as_cor_network correlate
-as_cor_network.correlate <- function(x, ...) {
-  cor_network(corr = x$r, p.value = x$p.value, ..., val.type = "list")
+as_cor_network.correlate <- function(x, directed = FALSE, ...) {
+  cor_network(corr = x$r, p.value = x$p.value, directed = directed, ...,
+              val.type = "list")
 }
 
 #' @rdname  as_cor_network
 #' @export
 #' @method as_cor_network rcorr
-as_cor_network.rcorr <- function(x, ...)
+as_cor_network.rcorr <- function(x, directed = FALSE, ...)
 {
   p.value <- x$P
   diag(p.value) <- 0
-  cor_network(corr = x$r, p.value = p.value, ..., val.type = "list")
+  cor_network(corr = x$r, p.value = p.value, directed = directed, ...,
+              val.type = "list")
 }
 
 #' @rdname  as_cor_network
 #' @export
 #' @method as_cor_network corr.test
-as_cor_network.corr.test <- function(x, ...)
+as_cor_network.corr.test <- function(x, directed = FALSE, ...)
 {
-  cor_network(corr = x$r, p.value = x$p, ..., val.type = "list")
+  cor_network(corr = x$r, p.value = x$p, directed = directed, ...,
+              val.type = "list")
 }
 
 #' @importFrom tibble as_tibble
-#' @importFrom igraph as_data_frame
+#' @importFrom igraph as_data_frame is.directed
 #' @rdname  as_cor_network
 #' @export
 #' @method as_cor_network igraph
@@ -139,7 +144,7 @@ as_cor_network.igraph <- function(x, ...)
   nodes <- tibble::as_tibble(igraph::as_data_frame(x, "vertices"))
   edges <- tibble::as_tibble(igraph::as_data_frame(x, "edges"))
   structure(.Data = list(nodes = nodes, edges = edges),
-            class = "cor_network")
+            directed = igraph::is.directed(x), class = "cor_network")
 }
 
 #' @rdname  as_cor_network

R/as-igraph.R

@@ -1,54 +1,58 @@
 #' Corece to a igraph object
 #' @description Functions to coerce a object to igraph if possible.
 #' @param x \code{R} object.
+#' @param directed 	logical value, whether or not to create a directed graph.
 #' @param ... extra params.
 #' @return igraph object.
 #' @importFrom igraph graph_from_data_frame as.igraph
 #' @rdname as_igraph
+#' @examples
+#' fortify_cor(mtcars) %>% as.igraph()
+#' correlate(mtcars, cor.test = TRUE) %>% as.igraph()
 #' @author Houyun Huang, Lei Zhou, Jian Chen, Taiyun Wei
 #' @export
-as.igraph.cor_tbl <- function(x, ...)
+as.igraph.cor_tbl <- function(x, directed = FALSE, ...)
 {
   x <- as_cor_network(x, ...)
-  igraph::graph_from_data_frame(x$edges, directed = FALSE,
+  igraph::graph_from_data_frame(x$edges, directed = directed,
                                 vertices = x$nodes)
 }
 
 #' @rdname  as_igraph
 #' @export
-as.igraph.mantel_tbl <- function(x, ...)
+as.igraph.mantel_tbl <- function(x, directed = FALSE, ...)
 {
-  as.igraph(as_cor_tbl(x), ...)
+  as.igraph(as_cor_tbl(x), directed = directed, ...)
 }
 
 #' @rdname  as_igraph
 #' @importFrom tidygraph tbl_graph
 #' @export
-as.igraph.rcorr <- function(x, ...)
+as.igraph.rcorr <- function(x, directed = FALSE, ...)
 {
   p.value <- x$P
   diag(p.value) <- 0
-  cor_network(x$r, p.value, ..., val.type = "igraph")
+  cor_network(x$r, p.value, directed = directed, ..., val.type = "igraph")
 }
 
 #' @rdname  as_igraph
 #' @export
-as.igraph.corr.test <- function(x, ...)
+as.igraph.corr.test <- function(x, directed = FALSE, ...)
 {
-  cor_network(x$r, x$p, ..., val.type = "igraph")
+  cor_network(x$r, x$p, directed = directed, ..., val.type = "igraph")
 }
 
 #' @rdname  as_igraph
 #' @export
-as.igraph.correlate <- function(x, ...)
+as.igraph.correlate <- function(x, directed = FALSE, ...)
 {
-  cor_network(x$r, x$p.value, ..., val.type = "igraph")
+  cor_network(x$r, x$p.value, directed = directed, ..., val.type = "igraph")
 }
 
 #' @importFrom igraph graph_from_data_frame
 #' @rdname  as_igraph
 #' @export
-as.igraph.cor_network <- function(x, ...)
+as.igraph.cor_network <- function(x, directed = FALSE, ...)
 {
-  igraph::graph_from_data_frame(x$edges, FALSE, x$nodes)
+  igraph::graph_from_data_frame(x$edges, directed, x$nodes)
 }

R/as-tbl-graph.R

@@ -1,54 +1,57 @@
 #' Corece to a graph_tbl object
 #' @description Functions to coerce a object to graph_tbl if possible.
 #' @param x \code{R} object.
+#' @param directed 	logical value, whether or not to create a directed graph.
 #' @param ... extra params.
 #' @return tbl_graph object.
 #' @importFrom tidygraph tbl_graph as_tbl_graph
 #' @rdname as_tbl_graph
 #' @author Houyun Huang, Lei Zhou, Jian Chen, Taiyun Wei
 #' @export
-as_tbl_graph.cor_tbl <- function(x, ...)
+as_tbl_graph.cor_tbl <- function(x, directed = FALSE, ...)
 {
   x <- as_cor_network(x, ...)
   tidygraph::tbl_graph(nodes = x$nodes,
-                       edges = x$edges, directed = FALSE)
+                       edges = x$edges, directed = directed)
 }
 
 
 #' @rdname  as_tbl_graph
 #' @export
-as_tbl_graph.mantel_tbl <- function(x, ...)
+as_tbl_graph.mantel_tbl <- function(x, directed = FALSE, ...)
 {
-  as_tbl_graph(as_cor_tbl(x), ...)
+  as_tbl_graph(as_cor_tbl(x), directed = directed, ...)
 }
 
 #' @rdname  as_tbl_graph
 #' @export
-as_tbl_graph.rcorr <- function(x, ...)
+as_tbl_graph.rcorr <- function(x, directed = FALSE, ...)
 {
   p.value <- x$P
   diag(p.value) <- 0
-  cor_network(x$r, p.value, ..., val.type = "tbl_graph")
+  cor_network(x$r, p.value, directed = directed, ..., val.type = "tbl_graph")
 }
 
 #' @rdname  as_tbl_graph
 #' @export
-as_tbl_graph.corr.test <- function(x, ...)
+as_tbl_graph.corr.test <- function(x, directed = FALSE, ...)
 {
-  cor_network(x$r, x$p, ..., val.type = "tbl_graph")
+  cor_network(x$r, x$p, directed = directed, ..., val.type = "tbl_graph")
 }
 
 #' @rdname  as_tbl_graph
 #' @export
-as_tbl_graph.correlate <- function(x, ...)
+as_tbl_graph.correlate <- function(x, directed = FALSE, ...)
 {
-  cor_network(x$r, x$p.value, ..., val.type = "tbl_graph")
+  cor_network(x$r, x$p.value, directed = directed, ..., val.type = "tbl_graph")
 }
 
 #' @importFrom tidygraph tbl_graph
 #' @rdname  as_tbl_graph
 #' @export
 as_tbl_graph.cor_network <- function(x, ...)
 {
-  tidygraph::tbl_graph(nodes = x$nodes, edges = x$edges, directed = FALSE)
+  directed <- attr(x, "directed")
+  tidygraph::tbl_graph(nodes = x$nodes, edges = x$edges,
+                       directed = directed %||% FALSE)
 }

R/cor-network.R

@@ -4,6 +4,7 @@
 #' @param x a cor_network object.
 #' @param corr correlation matrix.
 #' @param p.value significant matrix of correlation.
+#' @param directed 	logical value, whether or not to create a directed graph.
 #' @param row.names,col.names row and column names of correlation matrix.
 #' @param rm.dup logical (defaults to TRUE) indicating whether remove duplicate
 #'     rows. If TRUE, the correlation between A-B and B-A is retained only A-B.
@@ -44,6 +45,7 @@
 #' @export
 cor_network <- function(corr,
                         p.value = NULL,
+                        directed = FALSE,
                         row.names = NULL,
                         col.names = NULL,
                         rm.dup = TRUE,
@@ -107,9 +109,10 @@ cor_network <- function(corr,
   }
 
   switch (val.type,
-          tbl_graph = tidygraph::tbl_graph(nodes = nodes, edges = edges, directed = FALSE),
-          igraph    = igraph::graph_from_data_frame(edges, directed = FALSE, vertices = nodes),
-          list      = structure(.Data = list(nodes = nodes, edges  = edges), class = "cor_network")
+          tbl_graph = tidygraph::tbl_graph(nodes = nodes, edges = edges, directed = directed),
+          igraph    = igraph::graph_from_data_frame(edges, directed = directed, vertices = nodes),
+          list      = structure(.Data = list(nodes = nodes, edges  = edges),
+                                directed = directed, class = "cor_network")
   )
 }