plotMyMatrix.R

#' Plot an adjacency or incidence Matrix
#'
#' @param Mat  : a matrix representing the network
#' @param dimLabels : a vector of length 1 or 2 specifying the types of nodes in row and col  (functional group) (Default is \code{NULL})
#' @param clustering : a list of length 2 specifying a clustering on row and col
#' @param plotOptions : a list providing options. See details below.
#' @details The list of parameters \code{plotOptions} for the matrix plot is
#'  * "legend":  Boolean. Set TRUE if you want to see the legend. Default value is FALSE
#'  * "legend.title":  Boolean. Set TRUE if you want to print the title of the legend. Default value is FALSE
#'  * "legend.position":  Position of the legend. Possible values are 'bottom', 'top','left,'right'. Default value is 'bottom'
#'  * "rowNames":  Set true if the rownames must be plotted. Default value is FALSE
#'  * "colNames":  Set true if the colNames must be plotted. Default value is FALSE
#'  * "line.color":  Chain of character. The color of the lines to separate groups if a clustering is provided. Default value is red
#'  * "line.width":  Numeric. Width  of the lines to separate groups. Default value is NULL, automatically chosen
#'  * "title":  Chain of character. Title of the plot. Default value is NULL
#'
#' @return a ggplot object corresponding to the plot
#' @export
#'
#' @examples
#' M <- matrix(sample(c(0,1),900,replace=TRUE),30,30)
#' plotMyMatrix(M, dimLabels = c('individulals'), plotOptions= list(legend = FALSE))
#' M2 <- matrix( rpois(800,10),40,20)
#' plotMyMatrix(M2, dimLabels = c(row = 'reader',col = 'book'), plotOptions = list(legend = TRUE))
#'

plotMyMatrix = function(Mat, dimLabels = c(row = 'row', col = 'col'), clustering = NULL, plotOptions = NULL){


  if (length(dimLabels) == 1){dimLabels = rep(dimLabels,2); names(dimLabels)  =c('row','col')}
  if (is.null(names(dimLabels))){names(dimLabels) = c('row','col')}

  g <- plotMatrix(Mat, dimLabels = dimLabels, clustering, plotOptions)
  g
}