Description Usage Arguments Details Value Author(s)

Plotting parameters for iNZight Plots

1 | ```
inzpar(..., .viridis = requireNamespace("viridis", quietly = TRUE))
``` |

`...` |
If arguments are supplied, then these values are set. If left empty, then |

`.viridis` |
checks if the viridis package is installed; or can be turend off the default list is returned. |

A whole suite of parameters that can be used to fine-tune plots obtained from the
`iNZightPlot`

function.
The parameters include both plot type, style, and appearance.
They are described below.

- 'pch'
the plotting symbol to be used; default is '1' (empty circle)

- 'col.pt'
the colour of points. this can either be a single value, or a vector of colours if

`colby`

is specified- 'col.missing'
the colour for missing values; default is a light grey

- 'cex'
the overal scaling for the entire plot; values less than 1 will make the text and points smaller, while values larger than 1 will magnify everything

- 'cex.pt'
the scaling value for points

- 'cex.dotpt'
the scaling value for points in a dotplot. Note, this is not multiplicative with

`'cex.pt'`

- 'cex.lab'
the scaling value for the plot labels

- 'cex.axis'
the scaling value for the axis labels

- 'cex.main'
the scaling value for the main plot title

- 'cex.text'
the scaling value for text on the plot

- 'alpha'
transparency setting for points; default is 1, 0 is fully transparent

- 'bg'
the background color for the plot

- 'fill.pt'
the fill colour for points; default is

`"transparent"`

- 'lwd'
the line width of lines (for joining points)

- 'lty'
the line type of lines (for joining points)

- 'lwd.pt'
the line width used for points; default is 2

- 'col.line'
the colour of lines used to join points

- 'col.sub'
vector of up to two colours for the background of subplot labels. If only one specified, it is used for both.

- 'locate.col.def'
the default colour for locating points

- 'jitter'
the axes to add jitter to. Takes values

`"x"`

,`"y"`

, or`"xy"`

(default is en empty string,`""`

)- 'rugs'
the axes to add rugs to. Takes same values as

`jitter`

- 'trend'
a vector containing the trend lines to add to the plot. Possible values are

`c("linear", "quadratic", "cubic")`

- 'smooth'
the smoothing (lowess) for the points. Takes a value between 0 and 1 (the default, 0, draws no smoother)

- 'smoothby.lty'
the line type used for smoothers if

`trend.by = TRUE`

- 'quant.smooth'
if quantile smoothers are desired, they can be specified here as either the quantiles to smooth over (e.g.,

`c(0.25, 0.5, 0.75)`

), or`"default"`

, which uses the sample size to decide on an approprite set of quantile smoothers- 'LOE'
logical, if

`TRUE`

, then a 1-1 line of equality is drawn- 'join'
logical, if

`TRUE`

, then points are joined by lines- 'lines.by
logical, if

`join = TRUE`

and`colby`

is specified, points are joined by the specified variable- 'col.trend'
a named list of colors to be used for drawing the lines. The default is

`list(linear = "blue", quadratic = "red", cubic = "green4")`

- 'lty.trend'
a named list of line types for various types of trend lines. The default is

`list(linear = 1, quadratic = 2, cubic = 3)`

- 'trend.by'
logical, if

`TRUE`

, then trend lines are drawn separately for each group specified by`colby`

- 'trend.parallel'
logical, if

`TRUE`

, the trend lines by group are given the same slope; otherwise they are fit independently- 'col.smooth'
the colour of the smoother

- 'col.LOE'
the colour of the line of equality

- 'lty.LOE'
the line type of the line of equality

- 'boxplot'
logical, if

`TRUE`

, a boxplot is drawn with dotplots and histgrams- 'box.lwd', 'box.col', 'box.fill'
the line width, colour, and fill colour for the box plot drawn

- 'bar.lwd', 'bar.col', 'bar.fill'
the line width, colour, and fill colour of bars in a bar plot

- 'bar.counts'
logical, if

`TRUE`

bar graphs will display counts instead of percentages (the default)- 'full.height'
may no longer be necessary ...

- 'inf.lwd.comp', 'inf.lwd.conf'
the line width of comparison and confidence intervals, respectively

- 'inf.col.comp', 'inf.col.conf'
the colour of comparison and confidence intervals, respectively. These take a length 2 vector, where the first element is used for normal inference, while the second is used for bootstrap intervals

- 'inference.type'
the type of inference added to the plot. Possible values are

`c("comp", "conf")`

- 'inference.par'
the parameter which we obtain intervals for. For a dotplot or histogram, this can be either

`"mean"`

or`"median"`

; for bar plots it can be "proportion"- 'bs.inference'
logical, if

`TRUE`

, then nonparametric bootstrap simulation is used to obtain the intervals- 'min.count'
the min count for barplots inference; counts less than this are ignored

- 'n.boot'
the number of bootstrap simulations to perform

- 'large.sample.size'
sample sizes over this value will use a large-sample plot variant (i.e., scatter plots will become hex plots, dot plots become histograms)

- 'largesample'
logical, if

`TRUE`

, then the large-sample plot variance is used- 'scatter.grid.bins'
the number, N, of bins to use for the scatter-grid plot, producing an N x N matrix

- 'hex.bins'
the number of bins to use for hexagonal binning

- 'hex.style'
the style of the hexagons, one of "size" or "alpha"

- 'quant.cutoff'
if

`quant.smooth = "default"`

, these sample size values are used to determine which quantiles are drawn- 'plottype'
used to override the default plot type. Possible values, depending on data type, include

`c("scatter"|"grid"|"hex"|"dot"|"hist")`

- 'matchplots'
logical, if

`TRUE`

, then the type of plot is kept consistent between different subsets- 'match.limits'
a vector of two values used to decide whether to use all small-sample or all large-sample plots

- 'xlim'
a vector defining the x axis limits (default NULL will use the data)

- 'ylim'
a vector defining the y axis limits (default NULL will use the data)

- 'transform'
a list of variable transformations (e.g., list(x = 'log'))

- 'plot.features'
a list containing any additional features for new plots (e.g., maptype)

an object of class `inzpar.list`

tell029

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