boxplotCharacter: Box Plots

In MorphoTools2: Multivariate Morphometric Analysis

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", ...)

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.

Value

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

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 = "-")

## Not run: boxplotAll(centaurea, folderName = "../boxplots")

MorphoTools2 documentation built on March 7, 2023, 6:18 p.m.