args4devnboxes_plot {growthPheno}

Creates a list of the values for the options of profile plots for comparing smooths

Description

Creates a list of the values for the options of deviations boxplots for comparing smooths. Note that plots.by, facet.x and facet.y jointly define the organization of the plots. The default settings are optimized for traitSmooth so that, if you want to change any of these from their default settings when using args4devnboxes_plot with a function other than traitSmooth, then it is recommended that you specify all of them to ensure that the complete set has been correctly specified. Otherwise, the default settings will be those shown here and these may be different to the default settings shown for the function with which you are using args4devnboxes_plot.

Usage

args4devnboxes_plot(plots.by = "Type", 
                    facet.x = c("Method", "Tuning"), facet.y = ".", 
                    collapse.facets.x = TRUE, collapse.facets.y = FALSE, 
                    facet.labeller = NULL, facet.scales = "fixed", 
                    angle.x = 0, 
                    which.plots = "none", 
                    ggplotFuncs = NULL, 
                    ...)

Arguments

plots.by

A character that gives the names of the set of factors by which the data is to be grouped and a separate plot produced for each group. If NULL, no groups are formed. If a set of factors, such as Type, Tuning and Method, that uniquely index the combinations of the smoothing-parameter values is specified, then groups are formed for each combination of the levels of the these factors, and a separate plot is produced for each combination.

facet.x

A character giving the names of the factors to be used to form subsets to be plotted in separate columns of the profiles plots and deviations boxplots. The default of "." results in no split into columns.

facet.y

A character giving the factors to be used to form subsets to be plotted in separate rows of the profiles plots and deviations boxplots. The default of "." results in no split into rows.

collapse.facets.x

A logical to indicate whether all variables specified by facets.x are to be collapsed to a single variable. Note that the smoothing-parameters factors, if present, are always collapsed.

collapse.facets.y

A logical to indicate whether all variables specified by facets.y are to be collapsed to a single variable. Note that the smoothing-parameters factors, if present, are always collapsed.

facet.labeller

A ggplot function for labelling the facets of a plot produced using the ggplot function. For more information see ggplot.

facet.scales

A character specifying whether the scales are shared across all facets of a plot ("fixed"), or do they vary across rows (the default, "free_x"), columns ("free_y"), or both rows and columns ("free")?

angle.x

A numeric between 0 and 360 that gives the angle of the x-axis text to the x-axis. It can also be set by supplying, in ggplotFuncs, a theme function from ggplot2.

which.plots

A logical indicating which plots are to be produced. The options are either none or absolute.deviations and/or relative.deviations. Boxplots of the absolute deviations are specified by absolute.boxplots, the absolute deviations being the values of a trait minus their smoothed values (observed - smoothed). Boxplots of the relative deviations are specified by relative.boxplots, the relative deviations being the absolute deviations divided by the smoothed values of the trait.

ggplotFuncs

A list, each element of which contains the results of evaluating a ggplot function. It is created by calling the list function with a ggplot function call for each element. These functions are applied in creating the ggplot object for a boxplot.

...

allows arguments to be passed to other functions; not used at present.

Value

A named list.

Author(s)

Chris Brien

See Also

traitSmooth, probeSmooths, plotSmoothsComparison and args4chosen_plot.

Examples

args4devnboxes_plot(plots.by = "Type", 
                    facet.x = "Tuning", 
                    facet.y = c("Smarthouse", "Treatment.1"), 
                    which.plots = "absolute")