########################################################################
#
# John W. Emerson
# Department of Statistics
# Yale University
#
# Walton Green
# Department of Geology and Geophysics
# Yale University
#
########################################################################
########################################################################
## Copyright (C) 2006 John W. Emerson
##
## This document is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 2, or (at your option)
## any later version.
##
## This program is distributed in the hope that it will be useful, but
## WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
## General Public License for more details.
##
## A copy of the GNU General Public License is available via WWW at
## http://www.gnu.org/copyleft/gpl.html.  You can also obtain it by
## writing to the Free Software Foundation, Inc., 675 Mass Ave,
## Cambridge, MA 02139, USA.
##
## Bug reports to john.emerson@yale.edu
########################################################################
########################################################################
#
# library(vcd) contains a grid implementation of mosaic plots, an
# alternative to the default mosaicplot() originally implemented by
# Emerson and included in the base distribution.
#
# We extend the pairs() framework in a logical way: a data frame
# may contain any combination of continuous and categorical variables.
# Our pairs() tiles contain scatterplots, boxplot, or mosaic plots,
# as is appropriate.  Additional options are provided.
#
########################################################################
########################################################################
# gpairs		package:gpairs		R Documentation
#
# Generalized Pairs Plots
#
# Description:
#
#     Produces a matrix of plots showing pairwise relationships between
#     quantitative and categorical variables in a complex data set.
#
# Usage:
#
#     gpairs(x, ...)
#
#
# Arguments:
#
#     x:   a data frame (or matrix the relationships between whose columns are
#          to be examined). Any combination of quantitative and categorical
#          variables is acceptable.
#
#     outer.margins: a list of length 4 with units as components named
#          bottom, left, top, and right, giving the outer margins. Defaults
#          are two lines of text. TO DO: IF GIVEN AS A VECTOR
#          SHOULD BE FILLED IN WITH LINES AS DEFAULT UNIT.
#
#     outer.labels: default is NULL, for alternating axis labels around
#          the perimeter.  If 'all', all labels are printed, and if
#          'none' no labels are printed.
#
#     outer.rot: a 2-vector (x, y) rotating the left and right outer labels
#          x degrees and the top and bottom outer labels y degrees.  Only
#          implemented for scatterplot and boxplot tile axis labels.
#
#     gap: the gap between the tiles; defaulting to 0.05 of the width of a tile.
#          TO DO: CURRENTLY MUST BE A NUMBER INTERPRETED IN NPC UNITS.
#
#     buffer: the fraction by which to expand the range of quantitative
#          variables to provide plots that will not truncate plotting symbols.
#          Defaults to 0 (%) currently.  TODO: IMPLEMENT IN OTHER WAYS AND
#          suppert the same in barcode().
#
#     stat.pars: NULL
#          fontsize 7
#          signif 0.05
#
#     scatter.pars: NULL
#          pch 1
#          size unit(0.25, 'char')
#          col 'black'
#
#     bwplot.pars: NULL
#
#     stripplot.pars: NULL
#          pch 1
#          size unit(0.5, 'char')
#          col 'black'
#          jitter FALSE
#
#     mosaic.pars: NULL
#
#     axis.pars: NULL
#          n.ticks 5
#          fontsize 9
#
#     diag.pars: NULL
#          fontsize 9
#          show.hist TRUE
#          hist.color 'black'
#
#     upper.pars: NULL
#          lm.plot FALSE
#          ci.plot FALSE
#          loess.plot = FALSE
#          symlm.plot = FALSE
#          lm.stats = FALSE
#          corrgram = FALSE
#          barcode = TRUE
#          stripplot = FALSE
#
#     lower.pars: NULL
#          lm.plot = FALSE
#          ci.plot = FALSE
#          loess.plot = FALSE
#          symlm.plot = FALSE
#          lm.stats = FALSE
#          corrgram = FALSE
#          barcode = TRUE
#          stripplot = FALSE
#          qqplot = TRUE iff all other lower.pars are FALSE
#
#     whatis: FALSE
#
# Details:
#
#     Plotting viewport must be square, currently, because of problems with
#     rotations of mosaic tiles and barcodes.
#
# Value:
#
#     If whatis=TRUE, the value is a data frame containing variable names,
#     types, numbers of missing values, numbers of distinct values, precisions,
#     maxima and minima.
#
# Note:
#
# Author(s):
#
#     John Emerson and Walton Green
#
# See Also:
#
#    'pairs', 'mosaicplot', 'barcode', 'lattice:splom', 'vcd:strucplot', 'whatis'
#
# References:
#
#     "Mosaic Displays in S-PLUS: A General Implementation and a Case Study."
#         John W. Emerson, Statistical Computing and Graphics Newsletter, Vol. 9,
#         No. 1, 1988.
#     Graphical Analysis of Multiresponse Data:  Illustrated with a Plant
#         Breeding Trial.  Basford, K.E. and Tukey, J.W. (1999).
#     
#
# Examples:
#


source("barcode.txt")
source("gpairs.txt")
source("whatis.txt")

y <- data.frame(A=c(rep("red", 100), rep("blue", 100)),
                B=c(rnorm(100),round(rnorm(100,5,1),1)), C=runif(200),
                D=c(rep("big", 150), rep("small", 50)),
                E=rnorm(200))

gpairs(y, upper.pars=list(barcode=TRUE), whatis=TRUE)