ggvpc_xpose: VPC plot using ggplot2 (Xpose-alike version)

In qPharmetra/qpToolkit: qPharmetra R Tools

VPC plot using ggplot2 (Xpose-alike version)

Description

Plot basic vpc with 95% CI of 2.5th, 50th & 97.5th predicted percentile and observed data. This call is to be extended with for stratification, and axes definition using the layering custom to ggplot2 objects. See the examples below to learn more.

Usage

ggvpc_xpose(
  vpc,
  PI = c(0.025, 0.975),
  area.col.central = PI.ci.med.arcol,
  area.col.outer = gray(0.2),
  linetype.obs.central = "solid",
  linetype.obs.outer = "dashed",
  linecol.obs.central = PI.real.med.col,
  linecol.obs.outer = "darkslategrey",
  linesize.obs = 0.5,
  area.alpha = 0.33,
  point.shape = 1,
  point.size = 1.25,
  point.col = "darkslategrey",
  point.alpha = 0.5,
  yrange.stretch = c(0.9, 1.1),
  quiet = TRUE
)

Arguments

vpc	output from nm.read.vpc
PI	prediction interval (c(0.025,0.975) for 95% CI)
area.col.central	color of prediction polygon for the central tendency
area.col.outer	color of prediction polygon for the outer percentiles
linetype.obs.central	line type of central observed lines
linetype.obs.outer	line type of outer observed lines
linecol.obs.central	line color of central observed lines
linecol.obs.outer	line color of outer observed lines
linesize.obs	line width of observed data
area.alpha	area alpha transparancy scalar (between 0 and 1)
point.shape	numeric value for dot shape
point.size	scalar of the observed data dot size
point.col	color of observed data dots
point.alpha	point alpha transparancy scalar (between 0 and 1)
yrange.stretch	vector of c(min,max) which will proportionally rescale the lower and upper limits of the Y axis
quiet	whether to suppress process messages

Value

A ggplot object to be extended optionally

Note

Editing and stratification to be done by adding ggplot layer

See Also

nm.read.vpc, ggvpc_standard

Examples

library(ggplot2)
## example of vpc NOT involving stratification
 nm.read.vpc(path =  file.path(getOption("qpExampleDir"),"vpc_final_strt")) -> vpc.all

ggvpc_xpose(vpc.all) +
  labs(x = "Time (h)", y = "Concentration (ng/ml)")

ggvpc_xpose(vpc.all) +
  labs(x = "Time (h)", y = "Concentration (ng/ml)") +
  scale_y_log10() + scale_x_log10()

## demonstration of changing colors & stratification
ggvpc_xpose(vpc.all
            , area.col.outer = qp.green
            , area.col.central = qp.blue
            , area.alpha = 1
            , PI = c(0.05,0.95)) +
  labs(x = "Time (h)", y = "Concentration (ng/ml)") +
  scale_y_log10() + scale_x_log10() + facet_grid(~strata)

## PI smoothed
nm.read.vpc(path =  file.path(getOption("qpExampleDir"),"vpc_final_strt"),
PI.ci.area.smooth = TRUE) -> vpc.all
ggvpc_xpose(vpc.all
            , PI = c(0.05,0.95)) +
  labs(x = "Time (h)", y = "Concentration (ng/ml)") +
  scale_y_log10() + scale_x_log10() + facet_grid(~strata)

qPharmetra/qpToolkit documentation built on May 24, 2023, 8:52 a.m.