\name{pairs.CSP}
\alias{pairs.CSP}
%- Also NEED an `\alias' for EACH other topic documented here.
\title{Contour/Hexbin Scatterplot Matrices}
\description{
A pairs plotting of histograms and rectangular-binned or
hexagonal-binned image plots are produced using \code{hist} and
\code{ContourScatterPlot}, respectively.
}
\usage{
pairs.CSP(x,
status=NULL,
box.idx.list=NULL,
type.CSP=c("count.diff",
"p.hat",
"p.hat.norm",
"z.stat"),
alternate.hexbinplot=FALSE,
n.hexbins=100,
range.x=range(x),
varlabpos=round(seq(range.x[1],
ceiling(diff(range.x)/150)*150+range.x[1],
by=150),0),
cutoffs = seq(range.x[1],
ceiling(diff(range.x)/25)*25+range.x[1],
by=25),
labels = colnames(x),
panel = ContourScatterPlot,
main="",
image.col=heat.colors(10),
numlev=5,...,
lower.panel = legend.CSP,
upper.panel = panel,
overlay.panel=rect.box.idx,
border.boxes=1:length(box.idx.list),
lwd.boxes=rep(3,length(box.idx.list)),
lty.boxes=rep(1,length(box.idx.list)),
label.pos = 0.5,
cex.labels = NULL,
font.labels = 1,
row1attop = TRUE,
gap=1,
ch.col=c("heat.colors(n)",
"rainbow(n, start=.7, end=.1)",
"terrain.colors(n)",
"topo.colors(n)",
"cm.colors(n)"))
}
%- maybe also `usage' for other objects documented here.
\arguments{
\item{x}{matrix of data in which the columns are the variables and the
rows are the individual observations}
\item{status}{ numerical binary 0, 1 vector denoting the status of the
observations; default is NULL}
\item{box.idx.list}{a list of vectors indicating the positions of
'x' which form a box to be overlayed on the binned plot in the upper
and lower panels of the hexbin plot and the only the upper panel
of the rectangular-binned plot by default
}
\item{type.CSP}{character string denoting the type of value to be
estimated using the 'status' for each cell grid: the difference in
counts ("count.diff"), the proportion ("p.hat"), the normalized
proportion at 0.5 ("p.hat.norm"), the z.statistic ("z.stat"), see
\link{make.density} for details.}
\item{alternate.hexbinplot}{Boolean; if TRUE then alternate
hexbin pairs plot is used; otherwise the ContourScatterPlot with
rectangular bins is implemented}
\item{n.hexbins}{number of bins for hexbin call; default is 100}
\item{range.x}{vector denoting the min and the max of the observation
values across all variable columns}
\item{varlabpos}{vector of position of the variable values in which to
label the x and y axes }
\item{cutoffs}{the cutoffs for the x and y axes of the rectangular
bins when alternate.hexbinplot is FALSE}
\item{labels}{the labels for the diagonals when
alternative.hexbinplot is TRUE}
\item{panel}{default panel function; currently this is the
contour scatter plot with rectangular bins; this option is ignored
when 'alternate.hexbinplot' is TRUE}
\item{main}{the main title for the rectanglar Contour scatter plot
when alternative.hexbinplot is FALSE}
\item{image.col}{image colors for the rectangular bins when
alternative.hexbinplot is FALSE}
\item{numlev}{number of levels for the contours for the rectangular
bins when alternative.hexbinplot is FALSE}
\item{\dots}{other options in \code{hexagons} or \code{ContourScatterPlot}}
\item{lower.panel}{function for the lower panels of the pairs plot;
currently this is fixed as a hexbin (when
'alternate.hexbinplot' is TRUE) or the legend.CSP (when
'alternative.hexbinplot' is FALSE) }
\item{upper.panel}{function for the upper panels of the pairs plot;
currently this is fixed as a hexbin or contour scatter plot }
\item{overlay.panel}{Function which describes the overlay image on the
panels; currently this option only works with the 'rect.box.idx' function
and other functions that have the same signature}
\item{border.boxes}{vector of corresponding border colors for each of
the boxes in 'box.idx.list'}
\item{lwd.boxes}{vector of corresponding widths for each of the
outlined boxes in 'box.idx.list'; default is for all the boxes to
have lwd = 3}
\item{lty.boxes}{vector of corresponding line types for each of the
outlined boxes in 'box.idx.list'; default is for all the boxes to
have lty = 1}
\item{label.pos}{position of the labels on the diagonal panels which are
currently fixed as histograms; this option is not in use currently.}
\item{cex.labels}{ cex for the labels, used only when
'alternative.hexbinplot' is TRUE }
\item{font.labels}{ font for the labels, used only when
'alternative.hexbinplot' is TRUE }
\item{row1attop}{ boolean if row 1 is at the top, used only when
'alternative.hexbinplot' is TRUE }
\item{gap}{ used only when 'alternative.hexbinplot' is TRUE }
\item{ch.col}{character string denoting the type of color palette used
for the rectangular-binned image to be displayed in the legend when
'aternate.hexbinplot' is FALSE; default is "heat.colors(n)"}
}
\details{
There are no legends for the hexagonal (when 'alternate.hexbinplot' is
TRUE) but there is a roughly estimate legend available for the
rectangular binning (when 'alternate.hexbinplot' is FALSE) in the pairs plot.
}
\value{
A pairs plot is displayed. NOTE: The histograms on the diagonals are of the
whole dataset regardless of the value of the cells in each ContourScatterPlot.
}
\references{Hexbin, other papers.}
\author{J.Y. Wan and A.J. Rossini}
\seealso{objects to See Also as 'hexbin' in the \pkg{hexbin} package}
\examples{
if (interactive()){
if (require(rfcdmin)){
data.there<-is.element(c("st.1829", "unst.1829", "st.DRT",
"unst.DRT"),objects())
if ( ( sum(data.there) != length(data.there) )){
## obtaining the FCS objects from VRC data
data(VRCmin)
}
## subsetting the data for quicker plot display of less data
data.mat1<-st.DRT@data[1:10000, 1:5]
## hexagonal binning
pairs.CSP(data.mat1, alternate.hexbinplot=TRUE)
## rectangular binning with legends
pairs.CSP(data.mat1, numlev=3,
image.col=heat.colors(20))
## rectangular binning without legends
pairs.CSP(data.mat1, numlev=3,
image.col=heat.colors(20),
lower.panel=ContourScatterPlot)
## putting a box around the observations
## greater than 500 for the second variable
## less than 200 for the first variable
idx1<-which(data.mat1[,2] > 500) ## green box
idx2<-which(data.mat1[,1] < 200) ## blue box
box.idx.list<-list(idx1, idx2)
## hexbin plots
pairs.CSP(data.mat1, box.idx.list=box.idx.list,
alternate.hexbinplot=TRUE, border.vec=c("green", "blue"))
## rectangular binned plots
pairs.CSP(data.mat1, box.idx.list=box.idx.list,
alternate.hexbinplot=FALSE,border.vec=c("green", "blue"),
lower.panel=ContourScatterPlot)
}
}
}
\keyword{hplot}