verboseBoxplot {WGCNA}

Boxplot annotated by a Kruskal-Wallis p-value

Description

Plot a boxplot annotated by the Kruskal-Wallis p-value. Uses the function boxplot for the actual drawing.

Usage

verboseBoxplot(x, g, main = "", xlab = NA, ylab = NA, 
               cex = 1, cex.axis = 1.5, cex.lab = 1.5, cex.main = 1.5, 
               notch = TRUE, varwidth = TRUE, ...,
               addScatterplot = FALSE,
               pt.cex = 0.8, pch = 21, pt.col = "blue", pt.bg = "skyblue",
               randomSeed = 31425, jitter = 0.6)

Arguments

x

numerical vector of data whose group means are to be plotted

g

a factor or a an object coercible to a factor giving the groups that will go into each box.

main

main title for the plot.

xlab

label for the x-axis.

ylab

label for the y-axis.

cex

character expansion factor for plot annotations.

cex.axis

character expansion factor for axis annotations.

cex.lab

character expansion factor for axis labels.

cex.main

character expansion factor for the main title.

notch

logical: should the notches be drawn? See boxplot and boxplot.stats for details.

varwidth

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

...

other arguments to the function boxplot. Of note is the argument las that specifies label orientation. Value las=1 will result in horizontal labels (the default), while las=2 will result in vertical labels, useful when the labels are long.

addScatterplot

logical: should a scatterplot of the data be overlaid?

pt.cex

character expansion factor for the points.

pch

shape code for the points.

pt.col

color for the points.

pt.bg

background color for the points.

randomSeed

integer random seed to make plots reproducible.

jitter

amount of random jitter to add to the position of the points along the x axis.

Value

Returns the value returned by the function boxplot.

Author(s)

Steve Horvath, with contributions from Zhijin (Jean) Wu and Peter Langfelder

See Also

boxplot