#' Template parameters
#'
#' Template parameters to be imported into other function documentation. This
#' is not intended to be a stand-alone help file.
#'
#' @param network a list of interaction networks, one for each dataset. Each
#' entry of the list should be a \eqn{n * n} matrix or where each element
#' contains the edge weight between nodes \eqn{i} and \eqn{j} in the inferred
#' network for that dataset.
#' @param data a list of matrices, one for each dataset. Each entry of the list
#' should be the data used to infer the interaction \code{network} for that
#' dataset. The columns should correspond to variables in the data
#' (nodes in the network) and rows to samples in that dataset.
#' @param correlation a list of matrices, one for each dataset. Each entry of
#' the list should be a \eqn{n * n} matrix where each element contains the
#' correlation coefficient between nodes \eqn{i} and \eqn{j} in the
#' \code{data} used to infer the interaction network for that dataset.
#' @param moduleAssignments a list of vectors, one for each \emph{discovery}
#' dataset, containing the module assignments for each node in that dataset.
#' @param modules a list of vectors, one for each \code{discovery} dataset,
#' of modules to perform the analysis on. If unspecified, all modules
#' in each \code{discovery} dataset will be analysed, with the exception of
#' those specified in \code{backgroundLabel} argument.
#' @param backgroundLabel a single label given to nodes that do not belong to
#' any module in the \code{moduleAssignments} argument. Defaults to "0". Set
#' to \code{NULL} if you do not want to skip the network background module.
#' @param discovery a vector of names or indices denoting the \emph{discovery}
#' dataset(s) in the \code{data}, \code{correlation}, \code{network},
#' \code{moduleAssignments}, \code{modules}, and \code{test} lists.
#' @param test a list of vectors, one for each \code{discovery} dataset,
#' of names or indices denoting the \emph{test} dataset(s) in the \code{data},
#' \code{correlation}, and \code{network} lists.
#' @param verbose logical; should progress be reported? Default is \code{TRUE}.
#'
#' @name common_params
#' @keywords internal
NULL
#' Template parameters
#'
#' Template parameters to be imported into other function documentation. This
#' is not intended to be a stand-alone help file.
#'
#' @param simplify logical; if \code{TRUE}, simplify the structure of the output
#' list if possible (see Return Value).
#'
#' @name simplify_param
#' @keywords internal
NULL
#' Template parameters
#'
#' Template parameters to be imported into other function documentation. This
#' is not intended to be a stand-alone help file.
#'
#' @param orderModules logical; if \code{TRUE} modules ordered by clustering
#' their summary vectors. If \code{FALSE} modules are returned in the order
#' provided.
#'
#' @name orderModules_param
#' @keywords internal
NULL
#' Template parameters
#'
#' Template parameters to be imported into other function documentation. This
#' is not intended to be a stand-alone help file.
#'
#' @param orderNodesBy \code{NULL} (default), \code{NA}, or a vector of dataset
#' names or indices. Controls how nodes are ordered on the plot (see details).
#' @param orderSamplesBy \code{NULL} (default), \code{NA}, or a vector
#' containing a single dataset name or index. Controls how samples are ordered
#' on the plot (see details).
#' @param plotNodeNames logical; controls whether the node names are
#' drawed on the bottom axis.
#' @param plotSampleNames logical; controls whether the sample names are
#' drawed on the left axis.
#' @param plotModuleNames logical; controls whether module names are drawed.
#' The default is for module names to be drawed when multiple \code{modules}
#' are drawn.
#' @param main title for the plot.
#' @param main.line the number of lines into the top margin at which the plot
#' title will be drawn.
#' @param drawBorders logical; if \code{TRUE}, borders are drawn around the
#' \emph{weighted degree}, \emph{node conribution}, and \emph{module summary}
#' bar plots.
#' @param lwd line width for borders and axes.
#' @param naxt.line the number of lines into the bottom margin at which the node
#' names will be drawn.
#' @param saxt.line the number of lines into the left margin at which the sample
#' names will be drawn.
#' @param maxt.line the number of lines into the bottom margin at which the
#' module names will be drawn.
#' @param xaxt.line the number of lines into the bottom margin at which the
#' x-axis tick labels will be drawn on the module summary bar plot.
#' @param xaxt.tck the size of the x-axis ticks for the module summary bar
#' plot.
#' @param xlab.line the number of lines into the bottom margin at which the
#' x axis label on the \emph{module summary} bar plot(s) will be drawn.
#' @param yaxt.line the number of lines into the left margin at which the
#' y-axis tick labels will be drawn on the weighted degree and node
#' contribution bar plots.
#' @param ylab.line the number of lines into the left margin at which the
#' y axis labels on the \emph{weighted degree} and \emph{node contribution}
#' bar plots will be drawn.
#' @param yaxt.tck the size of the y-axis ticks for the weighted degree and
#' node contribution bar plots.
#' @param laxt.line the distance from the legend to draw the legend axis
#' labels, as multiple of \code{laxt.tck}.
#' @param laxt.tck size of the ticks on each axis legend relative to the
#' size of the correlation, edge weights, and data matrix heatmaps.
#' @param legend.main.line the distance from the legend to draw the legend
#' title.
#' @param cex.axis relative size of the node and sample names.
#' @param cex.lab relative size of the module names and legend titles.
#' @param cex.main relative size of the plot titles.
#' @param dataCols a character vector of colors to create a gradient from for
#' the data heatmap (see details). Automatically determined if \code{NA} or
#' \code{NULL}.
#' @param dataRange the range of values to map to the \code{dataCols} gradient
#' (see details). Automatically determined if \code{NA} or \code{NULL}.
#' @param corCols a character vector of colors to create a gradient from for
#' the correlation structure heatmap (see details).
#' @param corRange the range of values to map to the \code{corCols} gradient
#' (see details).
#' @param netCols a character vector of colors to create a gradient from for
#' the network edge weight heatmap (see details).
#' @param netRange the range of values to map to the \code{corCols} gradient
#' (see details). Automatically determined if \code{NA} or \code{NULL}.
#' @param degreeCol color to use for the weighted degree bar plot.
#' @param contribCols color(s) to use for the node contribution bar plot
#' (see details).
#' @param summaryCols color(s) to use for the node contribution bar plot
#' (see details).
#' @param naCol color to use for missing nodes and samples on the data,
#' correlation structure, and network edge weight heat maps.
#' @param dryRun logical; if \code{TRUE}, only the axes and labels will be
#' drawed.
#'
#' @name plot_params
#' @keywords internal
NULL
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