% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plot.crit.fun.R, R/plot.mat.nm.R,
%   R/plot.opt.more.par.R, R/plot.opt.more.par.mode.R, R/plot.opt.par.R,
%   R/plot.opt.par.mode.R, R/plotMat.R
\encoding{UTF-8}
\name{plot.critFun}
\alias{plot.critFun}
\alias{plot.crit.fun}
\alias{plotMatNm}
\alias{plot.optMorePar}
\alias{plot.opt.more.par}
\alias{plot.optMoreParMode}
\alias{plot.opt.more.par.mode}
\alias{plot.optPar}
\alias{plot.opt.par}
\alias{plot.optParMode}
\alias{plot.opt.par.mode}
\alias{plotMat}
\alias{plotArray}
\alias{plot.mat}
\title{Functions for plotting a partitioned matrix (representing the network)}
\usage{
\method{plot}{critFun}(x, main = NULL, ...)

\method{plot}{crit.fun}(x, main = NULL, ...)

plotMatNm(
  M = x,
  x = M,
  ...,
  main.title = NULL,
  title.row = "Row normalized",
  title.col = "Column normalized",
  main.title.line = -2,
  par.set = list(mfrow = c(1, 2))
)

\method{plot}{optMorePar}(x, main = NULL, which = 1, ...)

\method{plot}{opt.more.par}(x, main = NULL, which = 1, ...)

\method{plot}{optMoreParMode}(x, main = NULL, which = 1, ...)

\method{plot}{opt.more.par.mode}(x, main = NULL, which = 1, ...)

\method{plot}{optPar}(x, main = NULL, which = 1, ...)

\method{plot}{opt.par}(x, main = NULL, which = 1, ...)

\method{plot}{optParMode}(x, main = NULL, which = 1, ...)

\method{plot}{opt.par.mode}(x, main = NULL, which = 1, ...)

plotMat(
  x = M,
  clu = NULL,
  orderClu = FALSE,
  M = x,
  ylab = "",
  xlab = "",
  main = NULL,
  print.val = !length(table(M)) <= 2,
  print.0 = FALSE,
  plot.legend = !print.val && !length(table(M)) <= 2,
  print.legend.val = "out",
  print.digits.legend = 2,
  print.digits.cells = 2,
  print.cells.mf = NULL,
  outer.title = FALSE,
  title.line = ifelse(outer.title, -1.5, 7),
  mar = c(0.5, 7, 8.5, 0) + 0.1,
  cex.val = "default",
  val.y.coor.cor = 0,
  val.x.coor.cor = 0,
  cex.legend = 1,
  legend.title = "Legend",
  cex.axes = "default",
  print.axes.val = NULL,
  print.x.axis.val = !is.null(colnames(M)),
  print.y.axis.val = !is.null(rownames(M)),
  x.axis.val.pos = 1.01,
  y.axis.val.pos = -0.01,
  cex.main = par()$cex.main,
  cex.lab = par()$cex.lab,
  yaxis.line = -1.5,
  xaxis.line = -1,
  legend.left = 0.4,
  legend.up = 0.03,
  legend.size = 1/min(dim(M)),
  legend.text.hor.pos = 0.5,
  par.line.width = 3,
  par.line.width.newSet = par.line.width[1] * 2,
  par.line.col = "blue",
  par.line.col.newSet = "red",
  IM.dens = NULL,
  IM = NULL,
  wnet = NULL,
  wIM = NULL,
  use.IM = length(dim(IM)) == length(dim(M)) | !is.null(wIM),
  dens.leg = c(null = 100, nul = 100),
  blackdens = 70,
  plotLines = FALSE,
  frameMatrix = TRUE,
  x0ParLine = -0.1,
  x1ParLine = 1,
  y0ParLine = 0,
  y1ParLine = 1.1,
  colByUnits = NULL,
  colByRow = NULL,
  colByCol = NULL,
  mulCol = 2,
  joinColOperator = "+",
  colTies = FALSE,
  maxValPlot = NULL,
  printMultipliedMessage = TRUE,
  replaceNAdiagWith0 = TRUE,
  colLabels = FALSE,
  MplotValues = NULL,
  ...
)

plotArray(
  x = M,
  M = x,
  IM = NULL,
  ...,
  main.title = NULL,
  main.title.line = -2,
  mfrow = NULL
)

\method{plot}{mat}(
  x = M,
  clu = NULL,
  orderClu = FALSE,
  M = x,
  ylab = "",
  xlab = "",
  main = NULL,
  print.val = !length(table(M)) <= 2,
  print.0 = FALSE,
  plot.legend = !print.val && !length(table(M)) <= 2,
  print.legend.val = "out",
  print.digits.legend = 2,
  print.digits.cells = 2,
  print.cells.mf = NULL,
  outer.title = FALSE,
  title.line = ifelse(outer.title, -1.5, 7),
  mar = c(0.5, 7, 8.5, 0) + 0.1,
  cex.val = "default",
  val.y.coor.cor = 0,
  val.x.coor.cor = 0,
  cex.legend = 1,
  legend.title = "Legend",
  cex.axes = "default",
  print.axes.val = NULL,
  print.x.axis.val = !is.null(colnames(M)),
  print.y.axis.val = !is.null(rownames(M)),
  x.axis.val.pos = 1.01,
  y.axis.val.pos = -0.01,
  cex.main = par()$cex.main,
  cex.lab = par()$cex.lab,
  yaxis.line = -1.5,
  xaxis.line = -1,
  legend.left = 0.4,
  legend.up = 0.03,
  legend.size = 1/min(dim(M)),
  legend.text.hor.pos = 0.5,
  par.line.width = 3,
  par.line.width.newSet = par.line.width[1] * 2,
  par.line.col = "blue",
  par.line.col.newSet = "red",
  IM.dens = NULL,
  IM = NULL,
  wnet = NULL,
  wIM = NULL,
  use.IM = length(dim(IM)) == length(dim(M)) | !is.null(wIM),
  dens.leg = c(null = 100, nul = 100),
  blackdens = 70,
  plotLines = FALSE,
  frameMatrix = TRUE,
  x0ParLine = -0.1,
  x1ParLine = 1,
  y0ParLine = 0,
  y1ParLine = 1.1,
  colByUnits = NULL,
  colByRow = NULL,
  colByCol = NULL,
  mulCol = 2,
  joinColOperator = "+",
  colTies = FALSE,
  maxValPlot = NULL,
  printMultipliedMessage = TRUE,
  replaceNAdiagWith0 = TRUE,
  colLabels = FALSE,
  MplotValues = NULL,
  ...
)
}
\arguments{
\item{x}{A result from a corresponding function or a matrix or similar object representing a network.}

\item{main}{Main title.}

\item{\dots}{Additional arguments to \code{plot.default} for \code{plotMat} and also to \code{plotMat} for other functions.}

\item{M}{A matrix or similar object representing a network - either \code{x} or \code{M} must be supplied - both are here to make the code compatible with generic and with older functions.}

\item{main.title}{Main title in \code{plotArray} version.}

\item{title.row}{Title for the row-normalized matrix in nm version}

\item{title.col}{Title for the column-normalized matrix in nm version}

\item{main.title.line}{The line in which main title is printed in \code{plotArray} version.}

\item{par.set}{A list of possible plotting parameters (to \code{par}) to be used in nm version}

\item{which}{Which (if there are more than one) of optimal solutions to plot.}

\item{clu}{A partition. Each unique value represents one cluster. If the network is one-mode,
then this should be a vector, else a list of vectors, one for each mode/set.}

\item{orderClu}{Should the partition be ordered before plotting. \code{FALSE} by default. If \code{TRUE}, \code{\link{orderClu}} is used (using default arguments) to order the clusters in a partition in "decreasing" (see \code{\link{orderClu}} for interpretation) order.}

\item{ylab}{Label for y axis.}

\item{xlab}{Label for x axis.}

\item{print.val}{Should the values be printed in the matrix.}

\item{print.0}{If \code{print.val = TRUE} Should the 0s be printed in the matrix.}

\item{plot.legend}{Should the legend for shades be plotted.}

\item{print.legend.val}{Should the values be printed in the legend.}

\item{print.digits.legend}{The number of digits that should appear in the legend.}

\item{print.digits.cells}{The number of digits that should appear in the cells (of the matrix and/or legend).}

\item{print.cells.mf}{If not \code{NULL}, the above argument is ignored, the cell values are printed as the cell are multiplied by this factor and rounded.}

\item{outer.title}{Should the title be printed on the 'inner' or 'outer' margin of the plot, default is 'inner' margin.}

\item{title.line}{The line (from the top) where the title should be printed. The suitable values depend heavily on the displayed type.}

\item{mar}{A numerical vector of the form \code{c(bottom, left, top, right)} which gives the lines of margin to be specified on the four sides of the plot.
The R default for ordinary  plots is \code{c(5, 4, 4, 2) + 0.1}, while this function default is \code{c(0.5, 7, 8.5, 0) + 0.1}.}

\item{cex.val}{The size of the values printed. The default is \code{10 / 'number of units'}.}

\item{val.y.coor.cor}{Correction for centering the values in the squares in y direction.}

\item{val.x.coor.cor}{Correction for centering the values in the squares in x direction.}

\item{cex.legend}{Size of the text in the legend.}

\item{legend.title}{The title of the legend.}

\item{cex.axes}{Size of the characters in axes. Default makes the cex so small that all categories can be printed.}

\item{print.axes.val}{Should the axes values be printed. Default prints each axis if \code{rownames} or \code{colnames} is not \code{NULL}.}

\item{print.x.axis.val}{Should the x axis values be printed. Default prints each axis if \code{rownames} or \code{colnames} is not \code{NULL}.}

\item{print.y.axis.val}{Should the y axis values be printed. Default prints each axis if \code{rownames} or \code{colnames} is not \code{NULL}.}

\item{x.axis.val.pos}{The x coordinate of the y axis values.}

\item{y.axis.val.pos}{The y coordinate of the x axis values.}

\item{cex.main}{Size of the text in the main title.}

\item{cex.lab}{Size of the text in matrix.}

\item{yaxis.line}{The position of the y axis (the argument 'line').}

\item{xaxis.line}{The position of the x axis (the argument 'line').}

\item{legend.left}{How much left should the legend be from the matrix.}

\item{legend.up}{How much up should the legend be from the matrix.}

\item{legend.size}{Relative legend size.}

\item{legend.text.hor.pos}{Horizontal position of the legend text (bottom) - 0 = bottom, 0.5 = middle,...}

\item{par.line.width}{The width of the line that separates  the partitions.}

\item{par.line.width.newSet}{The width of the line that separates  that separates the sets/modes - only used when \code{clu} is a list and \code{par.line.width} has length 1.}

\item{par.line.col}{The color of the line that separates the partitions.}

\item{par.line.col.newSet}{The color of the line that separates  that separates the sets/modes - only used when \code{clu} is a list and \code{par.line.col} has length 1.}

\item{IM.dens}{The density of shading lines in each block.}

\item{IM}{The image (as obtained  with \code{critFunC}) of the blockmodel. \code{dens.leg} is used to translate this image into \code{IM.dens}.}

\item{wnet}{Specifies which matrix (if more) should be plotted  - used if \code{M} is an array.}

\item{wIM}{Specifies which \code{IM} (if more) should be used for plotting. The default value is set to \code{wnet}) - used if \code{IM} is an array.}

\item{use.IM}{Specifies if \code{IM} should be used for plotting.}

\item{dens.leg}{It is used to translate the \code{IM} into \code{IM.dens}.}

\item{blackdens}{At which density should the values on dark colors  of lines be printed in white.}

\item{plotLines}{Should the lines in the matrix be printed. The default value is set to \code{FALSE}, best set to \code{TRUE} for very small networks.}

\item{frameMatrix}{Should the matrix be framed (if \code{plotLines} is \code{FALSE}). The default value is set to \code{TRUE}.}

\item{x0ParLine}{Coordinates for lines separating clusters.}

\item{x1ParLine}{Coordinates for lines separating clusters.}

\item{y0ParLine}{Coordinates for lines separating clusters.}

\item{y1ParLine}{Coordinates for lines separating clusters.}

\item{colByUnits}{Coloring units. It should be a vector of unit length.}

\item{colByRow}{Coloring units by rows. It should be a vector of unit length.}

\item{colByCol}{Coloring units by columns. It should be a vector of unit length.}

\item{mulCol}{Multiply color when joining with row, column. Only used when when \code{colByUnits} is not \code{NULL}.}

\item{joinColOperator}{Function to join \code{colByRow} and \code{colByCol}. The default value is set to \code{"+"}.}

\item{colTies}{If \code{TRUE}, ties are colored, if \code{FALSE}, 0-ties are colored.}

\item{maxValPlot}{The value to use as a maximum when computing colors (ties with maximal positive value are plotted  as black).}

\item{printMultipliedMessage}{Should the message '* all values in cells were multiplied by' be printed on the plot. The default value is set to \code{TRUE}.}

\item{replaceNAdiagWith0}{If \code{replaceNAdiagWith0 = TRUE} Should the \code{NA} values on the diagonal of a matrix be replaced with 0s.}

\item{colLabels}{Should the labels of units be colored. If \code{FALSE}, these are not colored, if \code{TRUE}, they are colored with colors of clusters as defined by palette.
This can be also a vector of colors (or integers) for one-mode networks or a list of two such vectors for two-mode networks.}

\item{MplotValues}{A matrix to strings to plot in cells. Only to be used if other values than those in the original matrix (\code{x} or \code{M} arguments) should be used. Defaults to \code{NULL}, in which case the valued from original matrix are plotted (if this is not prevented by some other arguments). Overrides all other arguments that deal with cell values (e.g. \code{print.digits.cells}). Sets \code{print.val} to \code{TRUE} and \code{plot.legend} to \code{FALSE}.}

\item{mfrow}{\code{mfrow} Argument to \code{par} - number of row and column plots to be plotted on one figure.}
}
\value{
The functions are used for their side effect - plotting.
}
\description{
The main function \code{plot.mat} or \code{plotMat} plots a (optionally partitioned) matrix.
If the matrix is partitioned, the rows and columns of the matrix are rearranged according to the partitions.
Other functions are only wrappers for \code{plot.mat} or \code{plotMat} for convenience when plotting the results of the corresponding functions.
The \code{plotMatNm} plots two matrices based on M, normalized by rows and columns, next to each other. The \code{plotArray} plots an array. \code{plot.mat.nm} has been replaced by \code{plotMatNm}.
}
\examples{
# Generation of the network
n <- 20
net <- matrix(NA, ncol = n, nrow = n)
clu <- rep(1:2, times = c(5, 15))
tclu <- table(clu)
net[clu == 1, clu == 1] <- rnorm(n = tclu[1] * tclu[1], mean = 0, sd = 1)
net[clu == 1, clu == 2] <- rnorm(n = tclu[1] * tclu[2], mean = 4, sd = 1)
net[clu == 2, clu == 1] <- rnorm(n = tclu[2] * tclu[1], mean = 0, sd = 1)
net[clu == 2, clu == 2] <- rnorm(n = tclu[2] * tclu[2], mean = 0, sd = 1)

# Ploting the network
plotMat(M = net, clu = clu, print.digits.cells = 3)
class(net) <- "mat"
plot(net, clu = clu)
# See corresponding functions for examples for other ploting
# functions
# presented, that are essentially only the wrappers for "plot.max"
}
\references{
\enc{Žiberna, A.}{Ziberna, A.} (2007). Generalized Blockmodeling of Valued Networks. Social Networks, 29(1), 105-126. doi: 10.1016/j.socnet.2006.04.002

\enc{Žiberna, A.}{Ziberna, A.} (2008). Direct and indirect approaches to blockmodeling of valued networks in terms of regular equivalence. Journal of Mathematical Sociology, 32(1), 57-84. doi: 10.1080/00222500701790207
}
\seealso{
\code{\link{critFunC}}, \code{\link{optRandomParC}}
}
\author{
\enc{Aleš Žiberna}{Ales Ziberna}
}
\keyword{graphs}
\keyword{hplot}