Plot PM_valid objects.
Usage
# S3 method for PM_valid
plot(
x,
type = "vpc",
tad = FALSE,
outeq = 1,
line = TRUE,
marker = TRUE,
legend = FALSE,
log = FALSE,
grid = TRUE,
xlab,
ylab,
title,
xlim,
ylim,
...
)
Arguments
- x
The name of an PM_valid data object generated by the make_valid function, which is usually called by the
$validate
method for PM_result objects.- type
Default is "vpc" for a visual predictive check, but could be "pcvpc" for a prediction-corrected visual predictive check, or "npde" for a normalized prediction distribution error analysis/plot. Choosing npde will call npde::plot.NpdeObject. To modify this plot, supply argmuents as a named list:
npde = (...)
. Available arguments are in the user manual for the npde package.- tad
Boolean operator to use time after dose rather than time after start. Default is
FALSE
.- outeq
Which output equation to plot. Default is 1.
- line
A list of three elements
$upper
,$mid
, and$lower
, each of which controls characteristics of corresponding quantiles. The arguments to each of these list elements map to several plotly attributes. Each can be a boolean value or a list.TRUE
will plot default characteristics.FALSE
will suppress quantile plots. The elements of the list for each argument are as follows:value
The quantile value. Default for lower is 0.025, mid is 0.5, and upper is 0.975.color
The color for both the 95%CI region around simulated quantile vs. time, and the color of the line for the observation quantile vs. time. Default for lower and upper is "dodgerblue" and for mid it is "red".dash
The style of the obervation quantile line. Seeplotly::schema()
, traces > scatter > attributes > line > dash > values. Default for lower and upper is "dash" and for mid it is "solid".width
Default is 1 for lower, mid, and upper.opacity
The opacity of the 95%CI region around simulated quantile vs. time. Default is 0.4 for lower, mid and upper, but can range between 0 (fully transparent) to 1 (fully opaque). Example:line = list(upper = list(value = 0.9, color = "red", dash = "longdash", opacity = 0.5, width = 2))
- marker
Controls the plotting symbol for observations. This argument maps to the plotly marker object. It can be boolean or a list.
TRUE
will plot the marker with default characteristics.FALSE
will suppress marker plotting. If a list, can control many marker characteristics, including overriding defaults. Use the plotlyplotly::schema()
command in the console and navigate to traces > scatter > attributes > marker to see all the ways the marker can be formatted. Most common will be:color
Marker color.symbol
Plotting character. Seeplotly::schema()
, traces > scatter > attributes > marker > symbol > values.size
Character size in points.opacity
Ranging between 0 (fully transparent) to 1 (fully opaque).line
A list of additional attributes governing the outline for filled shapes, most commonly color and width.
Example:
marker = list(color = "red", symbol = "triangle", opacity = 0.8, line = list(color = "black", width = 2))
- legend
Controls display of legend. This argument maps to the plotly layout showlegend and legend arguments. It is either a boolean operator (most common) or a list of parameters to be supplied to plotly. See
plotly::schema()
> layout > layoutAttributes > legend and showlegend for more details on the available options for formatting. If legend is supplied as a list, the plotly layout > layoutAttributes > showlegend value will be set toTRUE
automatically.Examples:
legend = T
legend = list(orientation = "h", font = list(color = "blue"))
Default is
FALSE
- log
Boolean operator to plot the y axis in log base 10. This argument maps to the the yaxis type value in the layout object in plotly. Use the plotly
plotly::schema()
command in the console and navigate to layout > layoutAttributes > yaxis > type.Example:
log = T
- grid
Controls grid display. This argument maps to the xaxis and yaxis layout objects in plotly. Use the plotly
plotly::schema()
command in the console and navigate to layout > layoutAttributes > xaxis or yaxis > gridcolor or gridwidth. It is a Boolean operator. IfFALSE
, no grid is plotted. IfTRUE
, the default color grey and width 1 will be plotted at major tick marks. If a list, color and width can be customized.Examples:
grid = F
grid = list(gridcolor = "black", gridwidth = 2)
- xlab
Value for x axis label. This argument maps to the the xaxis title element of the layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the axis, or it can be a list for greater control. Use the plotly
plotly::schema()
command in the console and navigate to layout > layoutAttributes > xaxis > title to see the ways to customize this axis label. In addition to the plotly attributes, a custom Pmetrics attributebold
may be included as a list element, either on its own or within the font list. The default forbold
isTRUE
.Examples:
xlab = "Time (h)"
xlab = list(text = "Time", bold = F, font = list(color = "red", family = "Arial", size = 10))
xlab = list(text = "Time", font = list(bold = T))
Default is "Time" or "Time after dose" if
tad = TRUE
.- ylab
Value for y axis label. This argument maps to the the yaxis title element of the layout object in plotly. See
xlab
for details. Ifxlab
is specified as a list with formatting, andylab
is simply a character label, then the formatting for thexlab
will be applied to theylab
. To formatylab
independently, specify a formatting list as forxlab
.Default is "Output".
- title
Plot title. This argument maps to the the title layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the plot title, or it can be a list for greater control. Use the plotly
plotly::schema()
command in the console and navigate to layout > layoutAttributes > title to see other ways to customize the title using lists as additional arguments. In addition to the plotly attributes, a custom Pmetrics attributebold
may be included as a list element. The default forbold
isTRUE
.Examples:
title = "Observed vs. Predicted"
title = list(text = "Raw Data", font = list(color = "red", family = "Arial", size = 10, bold = T))
Default is to have no title.
- xlim
Limits of the x axis as a vector. This argument maps to the the xaxis range in the layout object in plotly. Use the plotly
plotly::schema()
command in the console and navigate to layout > layoutAttributes > xaxis > range.Example:
xlim = c(0,1)
- ylim
Limits of the y axis as a vector. This argument maps to the the yaxis range in the layout object in plotly. Use the plotly
plotly::schema()
command in the console and navigate to layout > layoutAttributes > yaxis > range.Example:
ylim = c(0,100)
- ...
If
type
is not "npde", the following apply. Other attributes which can be passed to the layout > xaxis/yaxis in a plotly plot to further control formatting. Note thatlog
,xlab
,ylab
,xlim
, andylim
are all controlled by the layout object, but are provided throughout Pmetrics plotly function arguments as shortcuts that map to layout elements. Therefore, the dots argument should be used to specify other aspects of the x axis, y axis, or both. Seeplotly::schema()
layout > layoutAttributes > xaxis/yaxis for options. To add to single axis, name it as a list. If attributes are specified without an enclosing xaxis or yaxis list, they will be applied to both axes.Examples:
NPex$data$plot(xaxis = list(tickcolor = "black", tickfont = list(family = "Arial", size = 14, color = "black"))) #applies to x axis only
NPex$data$plot(linecolor = "red", ticks = "inside") #applies to both axes
. . However, if
type
is "npde", to modify the appearance of the plot, supply a list of options,npde = list(...)
. See the documentation for thetype
argument above.
Details
Generates a plot of outputs (typically concentrations) on the y axis and time
on the x axis. If tad
was set to TRUE
when make_valid was called, then time may be either absolute (default) or time
after dose, controlled by the tad
argument to this plot function.
The following items are included in the plot:
Observed outputs. These may be either as measured for
type = "vpc"
or prediction corrected fortype = "pcvpc"
. Format of the observations is controlled by themarker
argument. The default islist(color = "black", symbol = "circle-open", size = 8)
.Quantiles vs. time for observations. These are plotted by default as dashed blue lines for the 2.5th and 97.5th percentiles and a solid red line for the median. Formatting and the value for each quantile can be controlled with the
upper
,mid
, andlower
arguments.95% CI around the same quantiles of combined simulations from each subject. The values and formatting for these quantile CIs are the same as for the observations, and also controlled with the
upper
,mid
, andlower
arguments.
Good vpc/pcvpc plots are considered to be those where the quantile lines for the oberservations lie within the 95%CI quantile regions for simulations, indicated that the model is "centered" on the data and faithfully captures the variability in the data. For an npde plot, one expects to see approximately normally distributed normalized prediction errors.
See also
Other PMplots:
plot.MMopt()
,
plot.PM_cov()
,
plot.PM_cycle()
,
plot.PM_data()
,
plot.PM_final()
,
plot.PM_model()
,
plot.PM_op()
,
plot.PM_pta()
,
plot.PM_sim()
Examples
library(PmetricsData)
# VPC
NPex$valid$plot()
#> Error in eval(expr, envir, enclos): attempt to apply non-function
# pcVPC
NPex$valid$plot(type = "pcvpc")
#> Error in eval(expr, envir, enclos): attempt to apply non-function
# modify median line and marker
NPex$valid$plot(
line = list(mid = list(color = "orange", dash = "dashdot")),
marker = list(
color = "blue", size = 12, symbol = "diamond",
line = list(color = "navy")
)
)
#> Error in eval(expr, envir, enclos): attempt to apply non-function