list of the values for the options of profile plots for comparing smoothsCreates a list of the values for the options of profile plots for comparing smooths.
Note that plots.by, facet.x, facet.y and include.raw 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 args4profile_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 args4profile_plot.
args4profile_plot(plots.by = "Type",
facet.x = c("Method", "Tuning"), facet.y = ".",
include.raw = "facet.x",
collapse.facets.x = TRUE, collapse.facets.y = FALSE,
facet.labeller = NULL, facet.scales = "fixed",
breaks.spacing.x = -4, angle.x = 0,
colour = "black", colour.column = NULL,
colour.values = NULL, alpha = 0.3,
addMediansWhiskers = TRUE,
ggplotFuncs = NULL,
...)A named list.
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.
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.
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.
A character indicating whether plots of the
raw (unsmoothed) trait, corresponding to the plots of the smoothed traits,
are to be included in profile plots. The options are no, alone,
facet.x, or facet.y. That is, the plots of the raw traits are
plotted separately or as part of either facet.x or
facet.y.
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.
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.
A ggplot function for labelling the
facets of a plot produced using the ggplot function.
For more information see ggplot.
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")?
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.
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.
A character specifying a single colour to use in
drawing the lines for the profiles. If colouring according to the
values of a variable is required then use colour.column.
A character giving the name of a column
in data over whose values the colours of the lines are to be
varied. The colours can be specified using colour.values.
A character vector specifying the values of
the colours to use in drawing the lines for the profiles.
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.
A numeric specifying the degrees of
transparency to be used in plotting the responses.
It is a ratio in which the denominator specifies the number of
points (or lines) that must be overplotted to give a solid cover.
A logical indicating whether plots over
time of the medians and outer whiskers are to be added to the plot.
The outer whiskers are related to the whiskers on a box-and-whisker
and are defined as the median plus (and minus) 1.5 times the
interquartile range (IQR). Points lying outside the whiskers are
considered to be potential outliers.
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 profile plot.
allows arguments to be passed to other functions; not used at present.
Chris Brien
traitSmooth, probeSmooths, plotSmoothsComparison and args4chosen_plot.
args4profile_plot(plots.by = "Type",
facet.x = "Tuning", facet.y = c("Smarthouse", "Treatment.1"),
include.raw = "facet.x",
alpha = 0.4,
colour.column = "Method",
colour.values = c("orange", "olivedrab"))
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