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Plot the layout/data of a field experiment.

Source: R/desplot.R, R/ggdesplot.R
desplot.Rd

Use this function to plot the layout of a rectangular lattice field experiment and also the observed data values.

Usage

desplot(
  data,
  form = formula(NULL ~ x + y),
  num = NULL,
  num.string = NULL,
  col = NULL,
  col.string = NULL,
  text = NULL,
  text.string = NULL,
  out1 = NULL,
  out1.string = NULL,
  out2 = NULL,
  out2.string = NULL,
  dq = NULL,
  dq.string = NULL,
  col.regions = RedGrayBlue,
  col.text = NULL,
  text.levels = NULL,
  out1.gpar = list(col = "black", lwd = 3),
  out2.gpar = list(col = "yellow", lwd = 1, lty = 1),
  at,
  midpoint = "median",
  ticks = FALSE,
  flip = FALSE,
  main = NULL,
  xlab,
  ylab,
  shorten = "abb",
  show.key = TRUE,
  key.cex,
  cex = 0.4,
  strip.cex = 0.75,
  subset = TRUE,
  gg = FALSE,
  ...
)

ggdesplot(
  data,
  form = formula(NULL ~ x + y),
  num = NULL,
  num.string = NULL,
  col = NULL,
  col.string = NULL,
  text = NULL,
  text.string = NULL,
  out1 = NULL,
  out1.string = NULL,
  out2 = NULL,
  out2.string = NULL,
  dq = NULL,
  dq.string = NULL,
  col.regions = RedGrayBlue,
  col.text = NULL,
  text.levels = NULL,
  out1.gpar = list(col = "black", lwd = 3),
  out2.gpar = list(col = "yellow", lwd = 1, lty = 1),
  at,
  midpoint = "median",
  ticks = FALSE,
  flip = FALSE,
  main = NULL,
  xlab,
  ylab,
  shorten = "abb",
  show.key = TRUE,
  key.cex,
  cex = 0.4,
  strip.cex = 0.75,
  subset = TRUE,
  gg = FALSE,
  ...
)

Arguments

data

A data frame.

form

A formula like yield~x*y|location. Note x,y are numeric.

num

Bare name (no quotes) of the column of the data to use as a factor for number-coding the text in each cell.

num.string

String name of the column of the data to use as a factor for number-coding the text in each cell.

col

Bare name (no quotes) of the column of the data to use for color-coding the text shown in each cell.

col.string

String name of the column of the data to use for color-coding the text shown in each cell.

text

Bare name (no quotes) of the column of the data to use for the actual text shown in each cell.

text.string

String name of the column of the data to use for the actual text shown in each cell.

out1

Bare name (no quotes) of the column of the data to use for first-level outlining around blocks of cells.

out1.string

String name of the column of the data to use for first-level outlining around blocks of cells.

out2

Bare name (no quotes) of the column of the data to use for second-level outlining around blocks of cells.

out2.string

String name of the column of the data to use for second-level outlining around blocks of cells.

dq

Bare name (no quotes) of the column of the data to use for indicating bad data quality with diagonal lines. This can either be a numeric vector or a factor/text. Cells with 1/"Q"/"Questionable" have one diagonal line. Cells with 2/"B"/"Bad","S","Suppressed" have crossed diagonal lines.

dq.string

String name of the column of the data to use for indicating bad data quality with diagonal lines.

col.regions

Colors for the fill color of cells.

col.text

Vector of colors for text strings.

text.levels

Character strings to use instead of default 'levels'.

out1.gpar

A list of graphics parameters for first-level outlining. Can either be an ordinary list() or a call to gpar() from the grid package.

out2.gpar

Graphics parameters for second-level of outlining.

at

Breakpoints for the color ribbon. Use this instead of 'zlim'. Note: using 'at' causes 'midpoint' to be set to NULL.

midpoint

Method to find midpoint of the color ribbon. One of 'midrange', 'median, or a numeric value.

ticks

If TRUE, show tick marks along the bottom and left sides.

flip

If TRUE, vertically flip the image.

main

Main title.

xlab

Label for x axis.

ylab

Label for y axis.

shorten

Method for shortening text in the key, either 'abb', 'sub', 'no', or FALSE.

show.key

If TRUE, show the key on the left side. (This is not the ribbon.)

key.cex

Left legend cex.

cex

Expansion factor for text/number in each cell.

strip.cex

Strip cex.

subset

An expression that evaluates to logical index vector for subsetting the data.

gg

If TRUE, desplot() switches to ggdesplot().

...

Other.

Value

A lattice or ggplot2 object

Details

To create the plot using lattice graphics: 1. desplot(...).

To create the plot using ggplot2 graphics, use one of the following: 1. ggdesplot(...). 2. desplot(..., gg=TRUE). 3. options(desplot.gg=TRUE); desplot(...). Method 3 is useful to modify all results from existing scripts.

The lattice version is complete, mature, and robust. The ggplot2 version is incomplete. The legend can only show colors, and some function arguments are ignored. In general, lattice graphics are about 4-5 times faster than ggplot2 graphics. Not all lattice parameters are passed down to xyplot, but it is possible to make almost any change to the plot by assigning the desplot object to a variable and then edit the object by hand or use update to modify the object. Then print it manually. See the first example below.

Use col.regions to specify fill colors. This can either be a vector of colors or a function that produces a vector of colors. If the response variable is a factor and col.regions is a function, it will be ignored and the cells are filled with default light-colored backgrounds and a key is placed on the left. If the response variable is numeric, the cells are colored according to col.regions, and a ribbon key is placed on the right.

Use shorten='abb' (this is default) to shorten the cell text to 2 characters using the abbreviate function Use shorten='sub' to use a 3-character substring. Use shorten='no' or shorten=FALSE for no shortening.

Note that two sub-plots with identical levels of the split-plot factor can be adjacent to each other by virtue of appearing in different whole-plots. To correctly outline the split-plot factor, simply concatenate the whole-plot factor and sub-plot factor together.

To get a map of a field with a true aspect ratio (lattice version only), include 'aspect=ylen/xlen' in the call, where 'ylen' is the vertical length of the field and 'xlen' is the horizontal length of the field.

To call this function inside another function, you can hack like this: vr <- "yield"; vx <- "x"; vy <- "y"; eval(parse(text=paste("desplot(", vr, "~", vx, "*", vy, ", data=yates.oats)")))

References

K. Ryder (1981). Field plans: why the biometrician finds them useful. Experimental Agriculture, 17, 243–256.

Author

Kevin Wright

Examples

if(require(agridat)){

# Show how to customize any feature.  Here: make the strips bigger.
data(besag.met)
d1 <- desplot(besag.met, 
              yield ~ col*row|county, 
              main="besag.met",
              out1=rep, out2=block, out2.gpar=list(col="white"), strip.cex=2)
d1 <- update(d1, par.settings = list(layout.heights=list(strip=2)))
print(d1)

# Show experiment layout
data(yates.oats)
desplot(yates.oats, 
        yield ~ col+row, 
        out1=block, out2=gen)

desplot(yates.oats, 
        block ~ col+row, 
        col=nitro, text=gen, cex=1, out1=block,
        out2=gen, out2.gpar=list(col = "gray50", lwd = 1, lty = 1))

}
#> Loading required package: agridat