Simple plotting function for trait or density data

mapBtrait: plots contourlines of the dataset with data superimposed

Usage

mapBtrait (x = NULL, y = NULL, colvar = NULL, main = NULL, col = NULL, 
       colkey = list(length = 0.3, width = 0.5, cex.axis = 0.8,         
         cex.clab = par("cex.lab")), xlim = NULL, ylim = NULL,
         contours = NULL, draw.levels = FALSE, col.levels = NULL,
         key.levels = FALSE, lwd.levels = 1, axes = TRUE, frame.plot = TRUE, ...)

Arguments

x, y: coordinates of the points to plot.
colvar: color variable.
col: The colors used for the color variable. A vector; the default is jet.col(100).
colkey: specifications for the color key. See colkey. The color key will only be drawn if draw.levels = TRUE.
main: title of the plot.
xlim, ylim: (approximate) ranges of the plot. This is only approximate, as the actual ranges are tuned by the aspect ratio, which is calculated in the function.
contours: A list with x, y, and z that specifies the contours. Usually, z is the water depth. If NULL, the contour specification from dataset MWTL is used (MWTL$contours)
draw.levels: Whether or not the depth levels should be added; if FALSE only levels that are >= 0 will be added.
col.levels: Colors of the depth levels (only applicable if draw.levels=TRUE); the default is to have grey colors. Also allowed is a function that takes as input the number of colors - see last example.
lwd.levels: The line width of the depth lines.
key.levels: Whether to add a color key with the depth levels; only applicable if draw.levels=TRUE). This can be TRUE or FALSE, or a list that specifies the color key (see colkey).
axes, frame.plot: arguments to the main plotting function (that opens a window)
...: additional arguments passed to the plot function points2D, e.g. the type of symbol to use (pch, cex, ...), or whether to use log-transformed color variables (log="c").

Value

returns nothing

Author

Karline Soetaert <karline.soetaert@nioz.nl>

Note

This is a quick-and-dirty plotting function, and there may be better alternatives around.

To scale the x- and y-axis, the aspect ratio is estimated as: asp = 1/ cos((mean(ylim) * pi)/180).

Examples


MWTLabiotics <- merge(MWTL$stations, MWTL$abiotics)
with (MWTLabiotics, mapBtrait(x, y, colvar=depth, pch=18, cex=2, 
    contours=MWTL$contours, clab="m", main="Water depth"))


# Change the colorkey and the contours (use NSBS contours) 
with (MWTLabiotics, mapBtrait(x, y , colvar=depth, pch=18, cex=2, 
    clab="m", main="Water depth", contours=NSBS$contours,
    colkey = list(dist=-0.05, length=0.5, width=0.5, cex.axis=0.6)))


# zoom in on an area (not full control due to the overruling aspect ratio)
with (MWTLabiotics, mapBtrait(x, y , colvar=depth, pch=18, cex=2, 
    clab="m", main="Water depth", ylim=c(51, 54), xlim=c(3,5),
    colkey = list(dist=-0.08, length=0.5, width=0.5, cex.axis=0.6)))


# adding also the contours 
with (MWTLabiotics, mapBtrait(x, y, colvar=D50, contours=MWTL$contours,
        pch=18, cex=2, clab="micrometer", main="Median grain", 
        draw.levels=TRUE, 
        colkey = list(dist=-0.08, length=0.5, 
                      width=0.5, cex.axis=0.6)))


# adding also the contours with color key
# note: - main color key then positioned elsewhere (side=1)

# Use a different color scheme 
collev <- function(n) ramp.col(col=c("darkorange", "darkblue"), n=n)

with (MWTLabiotics, mapBtrait(x, y, colvar=D50, pch=18, cex=1.5, 
    clab=c("","micrometer"), main="Median grain", contours=MWTL$contours, 
    draw.levels=TRUE, key.levels=TRUE, col.levels=collev,
    colkey = list(side=1, dist=-0.08, length=0.25, 
                  width=0.5, cex.axis=0.6)))


# Change the appearance of the colorkey for levels: 
with (MWTLabiotics, mapBtrait(x, y, colvar=D50, contours=MWTL$contours,
    pch=18, cex=1.5, clab=c("grain size","micrometer"), 
    main="Median grain",  
    draw.levels=TRUE, key.levels=list(length=0.5, width=0.5), 
    col.levels=collev, colkey = list(side=1, dist=-0.08, length=0.25, 
                  width=0.5, cex.axis=0.6)))


# Show the depth contours
mapBtrait(contours=NSBS$contours, draw.levels=TRUE, key.levels=TRUE)


# Use a different color scheme 
collev <- function(n) ramp.col(col=c("darkgreen", "darkblue"), n=n)
mapBtrait(contours=NSBS$contours, draw.levels=TRUE, col.levels=collev,
  key.levels=TRUE)


#------------------------------
# log-transformed color variables
#------------------------------

# average densities of Abra alba in the MWTL data.
A.alba <- getDensity(descriptor  = MWTL$density$station,
                     averageOver = MWTL$density$year,
                     taxon       = MWTL$density$taxon, 
                     value       = MWTL$density$density,
                     subset      = MWTL$density$taxon == "Abra alba")
                     
# add positions of stations 
# all.x=TRUE: also stations without A.alba are selected
# the NAs are converted to 0

A.alba <- merge(MWTL$stations, A.alba, by=1, all.x=TRUE) 
A.alba$value[which(is.na(A.alba$value))] <- 0

# plot with density values log-transfored
# 0-values will be transformed to NAs in mapBtrait; 
# we set the NA color="grey"

mapBtrait(A.alba$x, A.alba$y, colvar=A.alba$value, pch=18, 
          cex=2, contours=MWTL$contours, NAcol="grey", log="c")