pmx_plot_individual: Individual plot

In ggPMX: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models

Individual plot

Description

Individual plot

Usage

pmx_plot_individual(
  ctr,
  which_pages = 1L,
  print = FALSE,
  dname,
  pred_line,
  ipred_line,
  point,
  is.legend,
  use.finegrid,
  bloq,
  filter,
  strat.facet,
  facets,
  strat.color,
  trans,
  pmxgpar,
  labels,
  axis.title,
  axis.text,
  ranges,
  is.smooth,
  smooth,
  is.band,
  band,
  is.draft,
  draft,
  is.identity_line,
  identity_line,
  scale_x_log10,
  scale_y_log10,
  color.scales,
  ...
)

Arguments

ctr	pmx controller
which_pages	integer page(s) to display, or character "all" to display all pages (argument previously called npage, now deprecated)
print	logical if TRUE the ouptut will be a print not a ggplot2. This is useful for rmarkdwon output to avoid verbose list index print.
dname	character name of dataset to be used. User can create his own dataset using set_data and pass it as dname to be plotted.
pred_line	list some ipred line geom properties aesthetics
ipred_line	list some pred line geom properties aesthetics
point	list some point geom properties aesthetics
is.legend	logical if TRUE add a legend
use.finegrid	logical if FALSE use predictions data set
bloq	pmxBLOQ object created by pmx_bloq. pmx_update parameters
filter	expression filter which will be applied to plotting data.
strat.facet	formula optional stratification parameter by facetting. This split plot by strats(each strat in a facet)
facets	list facet_wrap parameters.
strat.color	character optional stratification parameter by grouping. This will split the plot by group (color) of strat.
trans	character define the transformation to apply on x or y or both variables
pmxgpar	a object of class pmx_gpar possibly the output of the pmx_gpar: Shared basic graphics parameters
labels	list list containing plot and/or axis labels: title, subtitle, x , y
axis.title	list containing element_text attributes to customize the axis title. (similar to ggplot2 axis.title theme)
axis.text	list containing element_text attributes to customize the axis text (similar to ggplot2 axis.text theme)
ranges	list limits of x/y ranges
is.smooth	logical if set to TRUE add smooth layer
smooth	list geom_smooth graphical/smoothing fun parameters
is.band	logical if TRUE add horizontal band
band	list horizontal band parameters. geom_hline graphical parameters.
is.draft	logical if TRUE add draft layer
draft	list draft layer parameters. geom_text graphical parameters.
is.identity_line	logical if TRUE add an identity line
identity_line	listgeom_abline graphical parameters.
scale_x_log10	logical if TRUE use log10 scale for x axis.
scale_y_log10	logical if TRUE use log10 scale for y axis.
color.scales	list define scales parameter in case of strat.color pmx_settings
...	others graphics parameters passed : pmx_gpar internal function to customize shared graphical parameters individual generic object for individual plots. pmx_update function. individual parameters

Value

ggplot2 or list of ggplot2 objects

Examples

# basic use  ---------------------------------------

ctr <- theophylline()
ctr %>% pmx_plot_individual(which_pages = 1)
## multiple pages
ctr %>% pmx_plot_individual(which_pages = c(1, 3))
## change faceting
ctr %>% pmx_plot_individual(facets = list(nrow = 5, ncol = 5), which_pages = 2)


# update graphical parameter  ----------------------

## update labels
ctr %>% pmx_plot_individual(
  labels = list(title = "Custom individual plot")
)

## remove draft
ctr %>% pmx_plot_individual(is.draft = FALSE)

## Customize ipred_line with any geom_line parameter
ctr %>% pmx_plot_individual(
  pred_line = list(color = "red", linetype = 20, alpha = 0.5)
)

## Customize ipred_line with any geom_line parameter
ctr %>% pmx_plot_individual(
  ipred_line = list(size = 5)
)


## Customize any geom_point parameter
ctr %>% pmx_plot_individual(
  point = list(aes(alpha = DV), color = "green", shape = 4)
)


## legend

p <- ctr %>% pmx_plot_individual(
  is.legend=TRUE,
  point=list(shape=20),
  pred_line=list(linetype=6)
)

# # stratification  ----------------------------------
#
# ## continuous stratification
ctr %>% pmx_plot_individual(strat.color = "WT0")

# # subsetting  --------------------------------------
#
# ## we can use any expression involving the data
# ## filter and stratify
ctr %>% pmx_plot_individual(
  filter = SEX == 1, strat.facet = ~SEX, 
  facets = list(nrow = 5, ncol = 5))

# # transformation  --------------------------------------
#
# ## apply a log transformation in y
ctr %>% pmx_plot_individual(trans = "log10_y")
# ## apply a custonm trsnformation to normalize axis between 0 and 1

## get a list of parameter
p <- ctr %>% pmx_plot_individual(
  which_pages="all",
  point=list(shape=4,color='blue',size=10),
  facets = list(nrow = 5, ncol = 5),
  labels = list(title = "My individuals",x='my time',y='PD data')
) 

ggPMX documentation built on July 9, 2023, 7:45 p.m.