args4meddevn_plot {growthPheno}

Creates a list of the values for the options of median deviations plots for smooths

Description

Creates a list of the values for the options of median deviations plots for smooths. Note that the arguments plots.by, plots.group, 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 args4meddevn_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 args4meddevn_plot.

Usage

args4meddevn_plot(plots.by = NULL, plots.group = "Tuning", 
                  facet.x = c("Method","Type"), facet.y = ".",  
                  facet.labeller = NULL, facet.scales = "free_x",
                  breaks.spacing.x = -4, angle.x = 0, 
                  colour.values = NULL, shape.values = NULL, 
                  alpha = 0.5, 
                  propn.note = TRUE, propn.types = NULL, 
                  ggplotFuncs = NULL, 
                  ...)

Arguments

plots.by

A character that give the names of the set of factors by which medians deviations 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.

plots.group

A character that gives the names of the set of factors by which the subset of medians deviations data within a single facet in a single plot is to be grouped for plotting as separate lines.

facet.x

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

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")?

breaks.spacing.x

A numeric whose absolute values specifies the distance between breaks for the x-axis in a sequence beginning with the minimum x value and continuing up to the maximum x value. If it is negative, the breaks that do not have x values in data will be omitted. Minor breaks will be at half this value or, if these do not correspond to x-values in data when breaks.spacing.x is negative, have a spacing of one. Thus, when breaks.spacing.x is negative, grid lines will only be included for x-values that occur in data. These settings can be overwritten by supplying, in ggplotFuncs, a scale_x_continuous function from ggplot2.

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.

colour.values

A character vector specifying the values of the colours to use in drawing the lines for the medians deviations within a facet. If this is a named vector, then the values will be matched based on the names. If unnamed, values will be matched in order (usually alphabetical) within the limits of the scale.

shape.values

A numeric vector specifying the values of the shapes to use in drawing the points for the medians deviations within a facet. If this is a named vector, then the values will be matched based on the names. If unnamed, values will be matched in order.

alpha

A numeric specifying the degrees of transparency to be used in plotting a median deviations plot. It is a ratio in which the denominator specifies the number of points (or lines) that must be overplotted to give a solid cover.

propn.note

A logical indicating whether a note giving the proportion of the median value of the response for each time is to be included in the medians.deviations plots.

propn.types

A numeric giving, for each of the trait.types, the proportion of the median value of the response for each time to be used to plot envelopes in the median deviations plots. If set to NULL, the plots of the proprotion envelopes are omitted.

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 median-deviations plot.

...

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

Value

A named list.

Author(s)

Chris Brien

See Also

traitSmooth, probeSmooths and plotSmoothsMedianDevns.

Examples

args4meddevn_plot(plots.by = "Type", plots.group = "Tuning",  
                  facet.x = "Method", facet.y = ".",
                  propn.types = c(0.02,0.1, 0.2))