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R/miic.plot.R

@@ -4,10 +4,18 @@
 #' Export miic result for plotting (with igraph)
 #'
 #' @description This function creates an object built from the result returned
-#' by \code{\link{miic}} that is ready to be fed to igraph plotting method.
+#' by \code{\link{miic}} that is ready to be fed to the plotting method.
 #'
-#' @details See the details of specific function for each method.
-#' For igraph, see \code{\link{getIgraph}}.
+#' @details The behavior depends on the method used for the export.
+#'
+#' For igraph, edges attributes are passed to the igraph graph
+#' and can be accessed with e.g. \code{E(g)$partial_correlation}.
+#' See \code{\link{miic}} for more details on edge parameters.
+#' By default, edges are colored according to the partial correlation
+#' between two nodes conditioned on the conditioning set
+#' (negative is blue, null is gray and positive is red)
+#' and their width is based on the conditional mutual information
+#' minus the complexity cost.
 #'
 #' @param mo [a miic object, required]
 #'
@@ -152,7 +160,7 @@ export <- function (mo, method="igraph", pcor_palette=NULL,
   }
 
 #-------------------------------------------------------------------------------
-#' Igraph plotting function for miic
+#' Igraph export function for miic
 #'
 #' @description This functions returns an igraph object built from the result
 #' returned by \code{\link{miic}}.
@@ -174,6 +182,8 @@ export <- function (mo, method="igraph", pcor_palette=NULL,
 #'
 #' @return An igraph graph object.
 #'
+#' @noRd
+#'
 #' @seealso
 #' \code{\link{miic}} for details on edge parameters in the returned object,
 #' \code{\link[igraph]{igraph.plotting}} for the detailed description of the

R/write.cytoscape.R

@@ -18,6 +18,7 @@ fromStringToNumberArrowType <- function(val) {
 #' coordinate `x` and `y` for each node. The optional first column can contain
 #' node names. If node names is not given, the order of the input file will be
 #' assigned to the list of positions.
+#' @return None
 #' @export
 #' @useDynLib miic
 #' @md

R/write.style.R

@@ -1,7 +1,10 @@
 #' Style writing function for the miic network
-#' @description This function writes the  miic style for a correct visualization using the cytoscape tool (http://www.cytoscape.org/).
+#' @description This function writes the  miic style for a correct
+#' visualization using the cytoscape tool (http://www.cytoscape.org/).
 #' @details The style is written in the xml file format.
-#' @param file [a string] The file path of the output file (containing the file name without extension).
+#' @param file [a string] The file path of the output file (containing the
+#' file name without extension).
+#' @return None
 #' @export
 #' @useDynLib miic