Produces a heat-map plot of the p-values for pairwise differences between
predictions that is in a data.frame. The data.frame includes
two factors whose levels specify, for each p-value, which factor levels are
being compared.
# S3 method for data.frame
plotPvalues(object, p = "p", x, y,
gridspacing = 0, show.sig = FALSE, alpha = 0.10,
sig.size = 3, sig.colour = "black",
sig.face = "plain", sig.family = "",
triangles = "both",
title = NULL, axis.labels = NULL, axis.text.size = 12,
colours = RColorBrewer::brewer.pal(3, "Set2"),
ggplotFuncs = NULL, printPlot = TRUE, ...)An object of class "ggplot", which can be plotted using print or otherwise manipulated.
A data.frame containing the three columns specified by p, x
and y.
A character giving the name of the column in object that contains
the p-values to be plotted.
A character giving the name of the column in object that contains
the factor whose levels index the p-values that are to be plotted in the same column.
A character giving the name of the column in object that contains
the labels of the p-values that are to be plotted as the rows.
A numeric specifying the number(s) of rows and columns
that form groups in the grid of differences. This is most useful when
two or more factors index the rows and columns. If a single, nonzero
number, k say, is given then a grid line is placed after every
kth row and column. If a vector of values is given then the
number of grid lines is the length of the vector and the spacing between
each is specified by the elements of the vector.
A logical that specifies whether asterisks indicating the level
of significance are to be added to the plot. If they are then
`***' indicates that \(p \leq 0.001\),
`**' that \( 0.001 < p \leq 0.01\),
`*' that \( 0.01 < p \leq 0.05\)
`.' that \( 0.05 < p \leq 0.10\). The last is only
included for alpha = 0.10.
A numeric giving the significance level for testing
pairwise differences; must be 0.05 or 0.10.
A numeric specifying the size, in pts, of the
significance asterisks.
A character specifying the colour to use for the
significance asterisks.
A character specifying the font face for the significance
asterisks ("plain", "italic", "bold", "bold.italic").
A character specifying the font family for the significance
asterisks. The font families that are available depends on the system. For font
families other than the basic Postscript fonts, see the extrafont package.
A character indicating whether the plot should include the
lower, upper or both traingle(s). Here it is only used
to adjust gridlines for the omission of the diagonal.
A character string giving the main title for the plot.
A character string giving the label to use for both the x- and y-axis.
A numeric giving the size of the labels on the axes
of the heatmap.
A vector of of colours to be passed to the ggplot function
scale\_colour\_gradientn.
A list, each element of which contains the
results of evaluating a ggplot2 function.
It is created by calling the list function with
a ggplot2 function call for each element.
These functions are applied in creating the ggplot object.
A logical indicating whether or not the a plot is to be printed. This would
be used when just the returned ggplot object is required.
Provision for passsing arguments to functions called internally - not used at present.
Chris Brien
plotPvalues.alldiffs, allDifferences.data.frame, ggplot