%#
%# fields  is a package for analysis of spatial data written for
%# the R software environment.
%# Copyright (C) 2022 Colorado School of Mines
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%# Contact: Douglas Nychka,  douglasnychka@gmail.edu,
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\name{quilt.plot}
\alias{quilt.plot}
\alias{bubblePlot}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{Useful plots for visualizing irregular spatial data. }
\description{
Given a vector of z values associated with 2-d locations this 
function produces an 
image-like plot where the locations are discretized to a grid  and the z 
values are coded as a color level from a color scale. }
\usage{
quilt.plot(x, y, z, nx = 64, ny = 64,  grid = NULL, 
           add.legend=TRUE,add=FALSE, nlevel=64, 
           col = tim.colors(nlevel),
           nrow=NULL, ncol=NULL,FUN =
                 NULL, plot=TRUE, na.rm=FALSE, 
                 boundary.grid = FALSE, ...)
                 
bubblePlot(x, y, z, col = viridisLite::viridis(256), 
       zlim=NULL, horizontal = FALSE,
                 legend.cex = 1, legend.lab = NULL, legend.line = 2,
                 legend.shrink = 0.9, legend.width = 1.2, legend.mar =
                 ifelse(horizontal, 3.1, 5.1), axis.args = NULL,
                 legend.args = NULL, size = 1, add = FALSE,
                 legendLayout = NULL, highlight = TRUE, highlight.color
                 = "grey30", ...)

}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{x}{A vector of the x coordinates of the locations -or- a
     a 2 column matrix of the x-y coordinates. }
  \item{y}{A vector of the y coordinates -or- if the locations are passed 
in x the z vector  }
  \item{z}{Values of the variable to be plotted. For bubblePlot if a character or factor will be assigned colors based on the order of appearance.}
  \item{nlevel}{Number of color levels.}
  \item{nx}{Number of grid boxes in x if a grid is not specified.}
  \item{ny}{Number of grid boxes in y. }
  \item{nrow}{Depreciated, same as nx.}
  \item{ncol}{Depreciated same as ny. }
  \item{grid}{A grid in the form of a \code{grid list}.  }
  \item{add.legend}{If TRUE a legend color strip is added}
  \item{add}{If FALSE add to existing plot.}
  \item{col}{Color function or the color scale for the image, the   default is the tim.colors  function --
    a pleasing spectrum for quilt.plot and the  modern and versitle
     viridis for bubblePlot }
  \item{boundary.grid}{If FALSE the passed grid is considered to be the  midpoints of the grid cells. 
  If TRUE then these are assumed to define corners and the number of boxes is one less in each dimension.}
     
    \item{plot}{If FALSE just returns the image object instead of plotting it.}
    \item{FUN}{The function to apply to values that are common to a grid
    box. The default is to find the mean. (see \code{as.image}).}
    \item{na.rm}{If FALSE NAs are not removed from zand so a grid box
    even one of these values may be an NA. (See details below.)}
  \item{size}{Size of bubble dots in cex units. Can be a vector to procduce different size points in the scatterplot.}
  \item{zlim}{Numerical range to determine the colorscale. If omitted the range of z is used. }
  \item{\dots}{ for quilt.plot  arguments to be passed to the \code{image.plot}
  function. For bubblePlot arguments to be passed to the \code{plot}
  function if \code{add=FALSE}, the default and to the \code{points}
  function if \code{add=TRUE}.
  }
  
\item{horizontal}{
If false (default) legend will be a vertical strip on the right side. If
true the legend strip will be along the bottom.  
}

\item{highlight}{If TRUE will add a circle around the "bubble" in the color
\code{highlight.color}.
}


\item{highlight.color}{ Color of circle, default is a darker grey.}

\item{legend.cex}{Character expansion to change size of the legend
label.}

\item{legend.lab}{ Label for the axis of the color legend. Default is no
label as this is usual evident from the plot title.}

\item{legend.line}{Distance in units of character height 
(same as in \code{mtext})
 of the legend label from the 
color bar. Make this larger if the label collides with the color axis labels.}

\item{legend.mar}{
Width in characters of legend margin that has the axis. Default is 5.1 
for a vertical legend and 3.1 for a horizontal legend.}

\item{legend.shrink}{
 Amount to shrink the size of legend relative to the full height or width
of the plot.  
}

\item{legend.width}{
Width in characters of the legend strip. Default is 1.2, a little bigger
that the width of a character. }

\item{axis.args}{A list giving additional arguments for the \code{axis} function used to 
create the legend axis. (See examples in \code{\link{image.plot}}.)}

\item{legend.args}{The nuclear option: arguments for a complete specification of the 
legend label, e.g. if you need to the rotate text or other details.  This is in the form of a list and is just passed to the 
mtext function and you will need to give both the side and line arguments for positioning.  This usually will not be needed. 
(See examples in \code{\link{image.plot}} .)}
\item{legendLayout}{The list returned by \code{setupLegend} that has the legend information about positioning.}

}
\details{

\strong{quilt.plot} 
This function combines the discretization to an image by the function 
\code{as.image} and is then graphed by \code{image.plot}.
By default, locations that fall into the same grid box will have their
z values averaged. This also means that observations that are NA will
result in the grid box average also being NA and can produce unexpected
results because the NA patterns can dominate the figure. If you are
unsure of the effect  try \code{na.rm = TRUE} for a comparison.

A similar function exists in the lattice package and produces spiffy
looking plots. The advantage of this fields version is that it uses
the
standard R graphics functions and is written in R code. Also, the
aggregation to average values for z values in the same grid box allows
for different choices of grids. If two locations are very close,
separating them could result in very small boxes. 

Legend placement is never completely automatic. Place the 
legend independently for more control, perhaps using \code{image.plot}
in tandem with \code{split.screen} or enlarging the plot margin 
See \code{help(image.plot)} for examples of this function and these 
strategies.

\strong{bubblePlot} Why was this function was written for fields?
Certainly ggplot has many options for this kind of figure. 
To quote Tim Hoar a gifted data scientist and software engineer at NCAR:
"because we could".   It is a crisp
implementation of this type of plot using lower level fields functions.
The user may choose  simply to use the source code as the basis for
a more
detailed function. However, this is also a quick plot to introduce in teaching.

This function is experimental in the sense it explores setting
out a plotting region in advance of the actual plotting using R base graphics.
See the functions  \code{\link{setupLegend}} and  \code{\link{addLegend}}
for more details. Other graphics approaches in R such as ggplot determine
the plotting regions and layout based on having the entire figure
specification at hand. Although this a comprehensive solution it also seems
overkill to just add a lone color bar to annotate a plot. Moreover, and the graphics lower level functions
to add the color bar legend are already available from the image.plot functio.
}

\author{D.Nychka}
\seealso{ as.image, discretize.image, image.plot, lattice, persp, drape.plot,  } 
\examples{

data( ozone2)
# plot 16 day of ozone data set

quilt.plot( ozone2$lon.lat, ozone2$y[16,])
US( add=TRUE, col="grey", lwd=2)

bubblePlot( ozone2$lon.lat, ozone2$y[16,] )
US( add=TRUE, col="magenta", lwd=2)

# colors based on a factor or character vector
O3Levels<- cut( ozone2$y[16,], c( 0,40,60,80,Inf),
labels=c("low","bckgrd","med", "high"))
table( O3Levels)
bubblePlot( ozone2$lon.lat, O3Levels )
US( add=TRUE, col="magenta", lwd=2)

### adding a common legend strip "by hand"
## to a panel of plots 
## and a custom color table

coltab<- two.colors( 256, middle="grey50" )

par( oma=c( 0,0,0,5)) # save some room for the legend
set.panel(2,2)
zr<- range( ozone2$y, na.rm=TRUE)

for( k in 1:4){
quilt.plot( ozone2$lon.lat, ozone2$y[15+k,], add.legend=FALSE,
 zlim=zr, col=coltab, nx=40, ny=40)
US( add=TRUE)
}
par( oma=c(0,0,0,1))
image.plot(zlim=zr,legend.only=TRUE, col=coltab)
# may have to adjust number of spaces in oma to make this work.
#  adding some grid lines  and using the boundary.grid option
# note that in this case grid boxes drawn to match lon/lats
data( ozone2)
lon<- ozone2$lon.lat[,1]
lat<- ozone2$lon.lat[,2]
z<- ozone2$y[16,]

gridList<- list( x=-94 :-81, 
                 y= 36:45 ) 

quilt.plot( lon, lat, z, grid= gridList, boundary.grid = TRUE,
             col=viridis(256) )
# add some gird lines
xline( gridList$x , col="grey", lwd=1, lty=1)
yline( gridList$y, col="grey", lwd=1, lty=2)
}

\keyword{hplot}% at least one, from doc/KEYWORDS