MorphoTools2 (version 1.0.2.1)

boxplotCharacter: Box Plots

Description

These functions produce a box-and-whisker plot(s) of the given morphological character(s).

Usage

boxplotCharacter(object, character, outliers = TRUE, lowerWhisker = 0.05,
          upperWhisker = 0.95, col = "white", border = "black", main = character,
          cex.main = 1.5, xlab = NULL, ylab = NULL, frame = TRUE, pch = 8,
          horizontal = FALSE, varwidth = FALSE, ...)
boxplotAll(object, folderName = "boxplots", outliers = TRUE, lowerWhisker = 0.05,
      upperWhisker = 0.95, col = "white", border = "black", main = character,
      cex.main = 1.5, xlab = NULL, ylab = NULL, frame = TRUE, pch = 8,
      horizontal = FALSE, varwidth = FALSE, width = 480, height = 480, units = "px", ...)

Value

None. Used for its side effect of producing a plot(s).

Arguments

object

an object of class morphodata.

character

a morphological character used to plot boxplot.

folderName

folder to save produced boxplots.

outliers

logical, if TRUE, the outliers are drawn.

lowerWhisker

percentile to which the lower whisker is extended.

upperWhisker

percentile to which the upper whisker is extended.

col

background colour for the boxes.

border

colour of outliers and the lines.

frame

logical, if TRUE, a 'frame' (box around the plot) is drawn.

main

main title for the plot.

cex.main

magnification to be used for the main title.

pch

plotting symbol of the outliers.

xlab, ylab

title of the respective axes.

horizontal

logical, indicating if the boxplot should be horizontal.

varwidth

logical, if TRUE, the boxes are drawn with widths proportional to the square-roots of the number of observations in the groups.

width

the width of the figure.

height

the height of the figure.

units

the units in which height and width are given. Can be "px" (pixels, the default), "in" (inches), "cm" or "mm".

...

further arguments to be passed to boxplot or bxp.

Details

These functions modify the classical boxplot function to allow whiskers to be extended to the desired percentiles. By default, the whiskers are extended to the 5th and 95th percentiles, because of the trimmed range (without the most extreme 10% of values) use to be used in taxa descriptions, determination keys, etc. Box defines 25th and 75th percentiles, bold horizontal line shows median (50th percentile). Missing values are ignored.

The boxplotAll function produces boxplots for each morphological character and saves them to a folder defined by the folderName argument. If it does not exist, a new folder is created.

Examples

data(centaurea)

boxplotCharacter(centaurea, character = "ST", col = "orange", border = "red")

boxplotCharacter(centaurea, character = "ST", outliers = FALSE,
          lowerWhisker = 0.1, upperWhisker = 0.9)

boxplotCharacter(centaurea, "ST", varwidth = TRUE, notch = TRUE,
          boxwex = 0.4, staplewex = 1.3, horizontal = TRUE)

boxplotCharacter(centaurea, "ST", boxlty = 1, medlwd = 5,
          whisklty = 2, whiskcol = "red", staplecol = "red",
          outcol = "grey30", pch = "-")

if (FALSE) boxplotAll(centaurea, folderName = "../boxplots")