pm_opts: Set global plot options

In metrumresearchgroup/pmplots: Plots for Pharmacometrics

Set global plot options

Description

Set global plot options

Usage

pm_options(
  smooth.lwd = 1.35,
  smooth.col = .ggblue,
  smooth.lty = 2,
  smooth.method = "loess",
  scatter.size = 1.5,
  scatter.col = "black",
  scatter.alpha = 1,
  density.lwd = 1.35,
  density.col = .ggblue,
  density.lty = 2,
  hline.lwd = 1.35,
  hline.col = "darkgrey",
  hline.lty = 1,
  abline.lwd = 1.35,
  abline.col = "darkgrey",
  abline.lty = 1,
  histogram.fill = "black",
  histogram.alpha = 0.6,
  histogram.col = "white",
  boxplot.fill = "white",
  boxplot.alpha = 1,
  boxplot.hline.lwd = 1,
  boxplot.hline.lty = 2,
  boxplot.hline.col = "black",
  boxplot.outlier.shape = 19,
  qq.col = .ggblue,
  qq.alpha = 1,
  qq.size = 1.35,
  pairs.cor.size = 3,
  pairs.cor.prefix = "corr\n",
  pairs.cor.col = .ggblue,
  pairs.cor.fontface = "bold",
  pairs.cor.digits = 2,
  pairs.cor.shown = TRUE,
  axis.title.short = FALSE,
  time.unit = "hr"
)

pm_opts

pm

Arguments

smooth.lwd	line width for smoother
smooth.col	line color for smoother
smooth.lty	line type for smoother
smooth.method	method to use for creating smoother
scatter.size	point size for scatter plot
scatter.col	character name of color for scatter plot
scatter.alpha	transparency for points in scatter plot
density.lwd	line width for density plot on histogram
density.col	line color for density plot on histogram
density.lty	line type for density plot on histogram
hline.lwd	line width for horizontal reference line; see layer_h() and gh()
hline.col	line color for horizontal reference line; see layer_h() and gh()
hline.lty	line type for horizontal reference line; see layer_h() and gh()
abline.lwd	line width for diagonal reference line; see layer_a() and ga()
abline.col	line color for diagonal reference line; see layer_a() and ga()
abline.lty	line type for diagonal reference line; see layer_a() and ga()
histogram.fill	fill color for histograms
histogram.alpha	alpha value for histograms
histogram.col	line color for histograms
boxplot.fill	fill color for histograms
boxplot.alpha	alpha value for boxplots
boxplot.hline.lwd	line width for horizontal reference line
boxplot.hline.lty	line type for horizontal reference line
boxplot.hline.col	line color for horizontal reference line
boxplot.outlier.shape	shape for outliers in boxplots
qq.col	point color for qq plots
qq.alpha	alpha value for qq plots
qq.size	point size for qq plots
pairs.cor.size	font size for correlation text in upper panels of pairs plots
pairs.cor.prefix	prefix for correlation text in upper panels of pairs plots
pairs.cor.col	color for correlation text in upper panels of pairs plots
pairs.cor.fontface	font face for correlation text in upper panels of pairs plots
pairs.cor.digits	number of digits to show when reporting correlation in upper panels of pairs plots
pairs.cor.shown	if TRUE, then report the number of non-missing observations used to calculate correlation in upper panels of pairs plots
axis.title.short	shorten standard axis titles
time.unit	default time unit

Format

An object of class pm_opts (inherits from environment) of length 43.

An object of class pm_opts (inherits from environment) of length 43.

Details

pm() and pm_opts() both refer to the same environment.

Global options can be set in the environment with pm$set(name = value). There is also a .list argument to pm$set that allows you to pass in a named list of options to set (e.g. pm$set(.list = list(smooth.col="red4"))).

Values can be extracted with pm$get("name").

Because it is an environment, the $ operator can also be used to get and set values (see examples).

Other methods in the environment include pm$as.list(), pm$mget(), pm$reset(). pm$self refers to the environment itself. A list of default settings can be obtained with pm$defaults. Methods for the pm_opts object include: print.pm_opts, as.list.pm_opts, $<-.pm_opts.

Examples

pm$set(smooth.lwd = 2)

pm$smooth.lwd

pm$smooth.lwd <- 1.3

pm$smooth.lwd

pm$get("smooth.lwd")

pm$reset()

x <- pm$as.list()

## Not run: 
 defs <- pm$defaults
 defs$smooth.col <- "firebrick"
 pm$set(.list = defs)

## End(Not run)

metrumresearchgroup/pmplots documentation built on Oct. 15, 2024, noon