R/graphDGEobj.R

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

### Function mapDGEobj ###
#' Function mapDGEobj
#'
#' Reads a DGEobj and produces a node pair file defining parent/child relationships between
#' data items in the DGEobj.  Plot them with Function graphDGEobj.
#'
#' @author John Thompson, \email{jrt@@thompsonclan.org}
#' @keywords RNA-Seq, unit conversion
#'
#' @param DGEobj A workflow object of DGEobj class data.
#'
#' @return A class igraph network object.
#'
#' @examples
#'
#'   library(igraph)
#'   library(RColorBrewer)
#'
#'   # Prepare an iGraph object for plotting
#'   mynet <- mapDGEobj(dgeObj)
#'
#'   #define a layout
#'   lay.sug <- layout_with_sugiyama(mynet)
#'
#'   #2D Plot
#'   plot(mynet,
#'        edge.arrow.size=.3,
#'        vertex.color="dodgerblue2",
#'        vertex.frame.color="dodgerblue4",
#'        layout=lay.sug$layout)
#'
#'   #2D Plot; colorby the basetype attribute
#'   pal <- brewer.pal(length(unique(V(mynet)$basetype)), "Set1")
#'   myPallet <- pal[as.numeric(as.factor(vertex_attr(mynet, "basetype")))]
#'
#'   plot(mynet,
#'        edge.arrow.size=.3,
#'        vertex.color = myPallet,
#'        vertex.label.family = "Helvetica",
#'        layout=lay.sug$layout
#'        )
#'
#'   #2D Interactive plot
#'   plotHandle <- tkplot(net,
#'                        vertex.color=myPallet,
#'                        vertex.frame.color="dodgerblue4",
#'                        canvas.width = 800,
#'                        canvas.height = 800,
#'                        layout=lay.sug$layout)
#'   tk_close(plotHandle)
#'
#' @import magrittr
#' @importFrom DGEobj inventory
#' @importFrom assertthat assert_that
#' @importFrom igraph graph_from_data_frame
#'
#' @export
mapDGEobj <- function(dgeObj, directed=TRUE) {

  assertthat::assert_that(class(dgeObj)[[1]] == "DGEobj")

  # df <- DGEobj::inventory(dgeObj) %>%
  #   select(Child = ItemName, Parent)
  child <- names(dgeObj)
  parent <- attr(dgeObj, "parent") %>% as.character()
  type <- attr(dgeObj, "type") %>% as.character()
  basetype <- attr(dgeObj, "basetype") %>% as.character()
  edges <- as.data.frame(cbind(parent=parent,
               child=child),
               # type = as.character(type),
               # basetype = as.character(basetype)),
               stringsAsFactors=FALSE)
  #remove incomplete edges (children without parents)
  idx <- lapply(parent, nchar) != 0
  edges <- edges[idx,]

  nodes <-data.frame(node=names(dgeObj),
                     type = as.character(type),
                     basetype = as.character(basetype))

  igraph::graph_from_data_frame(d=edges, vertices=nodes, directed=directed)
}