plot_dist: Plot a distribution as a hybrid containing a halfeye, a...

In pmxTools: Pharmacometric and Pharmacokinetic Toolkit

Plot a distribution as a hybrid containing a halfeye, a boxplot and jittered points.

Description

Plot a distribution as a hybrid containing a halfeye, a boxplot and jittered points.

Usage

plot_dist(
  dat,
  yvar,
  xvar = NULL,
  ylim = NULL,
  xlb = "",
  ylb = "",
  identity_line = FALSE,
  identity_value = 0,
  he_adjust = 0.5,
  he_width = 0.6,
  he_justification = -0.2,
  he_col = "black",
  he_fill = "#F8766D",
  he_alpha = 0.9,
  he_slab_type = "pdf",
  he_breaks = "Sturges",
  he_outline_bars = FALSE,
  he_point_interval = "median_qi",
  bxp_width = 0.12,
  bxp_outlier_col = NA,
  bxp_outlier_fill = NA,
  bxp_outlier_shape = 19,
  bxp_outlier_size = 1.5,
  bxp_col = "black",
  bxp_fill = "#F8766D",
  bxp_alpha = 0.9,
  bxp_notch = FALSE,
  bxp_notchwidth = 0.5,
  hp_range_scale = 0.4,
  hp_alpha = 0.25,
  hp_col = "#F8766D",
  hp_transformation = position_jitter(),
  na.rm = FALSE
)

Arguments

dat	A data frame.
yvar	The name of the field containing values to be plotted.
xvar	The name of the field containing the grouping variable (defaults to 'NULL').
ylim	Limits for the y-axis. Defaults to NULL. If provided, should be a 2-element vector containing the upper and lower limits.
xlb	Label for the x-axis.
ylb	Label for the y-axis.
identity_line	Show a line of identity? Default FALSE.
identity_value	If an identity line is shown, it will be drawn horizontally at this y-value (default 0).
he_adjust	If he_slab_type is "pdf", bandwidth for the density estimator is adjusted by multiplying it by this value.
he_width	Width of the halfeye component of the plot (default 0.6).
he_justification	Justification of the halfeye component of the plot (default -0.2).
he_col	Color for the halfeye component of the plot.
he_fill	Fill color for the halfeye component of the plot.
he_alpha	Alpha for the halfeye component of the plot (default 0.9).
he_slab_type	The type of slab function to calculate for the halfeye component of the plot: probability density (or mass) function ("pdf", the default), cumulative distribution function ("cdf"), complementary CDF ("ccdf") or histogram ("histogram").
he_breaks	If slab_type is "histogram", the breaks parameter that is passed to hist() to determine where to put breaks in the histogram.
he_outline_bars	If slab_type is "histogram", determines if outlines in between the bars are drawn when the slab_color aesthetic is used. If FALSE (the default), the outline is drawn only along the tops of the bars; if TRUE, outlines in between bars are also drawn.
he_point_interval	A function from the ggdist::point_interval family (e.g., median_qi, mean_qi, mode_hdi, etc), or a string giving the name of a function from that family (e.g., "median_qi", "mean_qi", "mode_hdi", etc. This function determines the point summary (typically mean, median, or mode) and interval type (quantile interval, qi; highest-density interval, hdi; or highest-density continuous interval, hdci). Output will be converted to the appropriate x- or y-based aesthetics depending on the value of orientation.
bxp_width	Width of the boxplot component (default 0.12).
bxp_outlier_col	Color for outliers in the boxplot component.
bxp_outlier_fill	Fill color for outliers in the boxplot component.
bxp_outlier_shape	Shape for outliers in the boxplot component.
bxp_outlier_size	Size for outliers in the boxplot component.
bxp_col	Color for the boxplot component.
bxp_fill	Fill color for the boxplot component.
bxp_alpha	Alpha for the boxplot component.
bxp_notch	If FALSE (default) make a standard box plot. If TRUE, make a notched box plot. Notches are used to compare groups; if the notches of two boxes do not overlap, this suggests that the medians are significantly different.
bxp_notchwidth	For a notched box plot, width of the notch relative to the body (default 0.5).
hp_range_scale	If no 'width' argument is specified in hp_transformation, used to determine the width of the jitter. Defaults to 0.75, which is half of the allotted space for the jitter-points, whereas 1 would use all of the alotted space.
hp_alpha	Alpha for the jitter.
hp_col	Color for the jitter.
hp_transformation	An evaluated position_*() function yielding a 'Position' object with specified parameters to calculate the transformation of the points. Defaults to ggplot2::position_jitter.
na.rm	If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

Value

A plot containing jittered points, a boxplot and a density plot or histogram illustrating the distribution of every group of the data under evaluation.

Author(s)

Justin Wilkins, [e-mail]

Examples

## Not run: 
 plot_dist(dat, "ETA1", identity_line = T, he_slab_type = "histogram", he_breaks = 30)

## End(Not run)

pmxTools documentation built on March 7, 2023, 7:58 p.m.