plotBivariateDataViewer

Usage

plotBivariateDataViewer(
  obs1 = NULL,
  obs2 = NULL,
  settings = list(),
  stratify = list(),
  preferences = list()
)

Arguments

obs1

(character) Name of the observation to display in x axis (in dataset header). By default the first observation is considered.

obs2

(character) Name of the observation to display in y axis (in dataset header). By default the second observation is considered.

settings

List with the following settings

• dots (logical) - If TRUE individual observations are displayed as dots (default TRUE).

• lines (logical) - If TRUE individual observations are displayed as lines (default TRUE).

• legend (logical) add (TRUE) / remove (FALSE) plot legend (default FALSE).

• grid (logical) add (TRUE) / remove (FALSE) plot grid (default TRUE).

• xlog (logical) add (TRUE) / remove (FALSE) log scaling on x axis (default FALSE).

• ylog (logical) add (TRUE) / remove (FALSE) log scaling on y axis (default FALSE).

• xlab (character) label on x axis (Name of obs1 by default).

• ylab (character) label on y axis (Name of obs2 by default).

• ncol (integer) number of columns when facet = TRUE (default 4).

• xlim (c(double, double)) limits of the x axis.

• ylim (c(double, double)) limits of the y axis.

• fontsize (integer) Plot text font size.

• units (logical) Set units in axis labels (only available with PKanalix).

• scales (character) Should scales be fixed ("fixed"), free ("free", the default), or free in one dimension ("free_x", "free_y") (default "free").

stratify

List with the stratification arguments:

• groups - Definition of stratification groups. By default, stratification groups are already defined as one group for each category for categorical covariates, and two groups of equal number of individuals for continuous covariates. To redefine groups, for each covariate to redefine, specify a list with:

  name	character	covariate name (e.g "AGE")
  definition	(vector(continuous) || list>(categorical))	For continuous covariates, vector of break values (e.g c(35, 65)). For categorical covariates, groups of categories as a list of vectors(e.g list(c("study101"), c("study201","study202")))

• split (vector) - Vector of covariates used to split (i.e facet) the plot (by default no split is applied). For instance c("FORM","AGE").

• filter (list< list> >) - List of pairs containing a covariate name and the vector of indexes or categories (for categorical covariates) of the groups to keep (by default no filtering is applied). For instance, list("AGE",c(1,3)) to keep the individuals belonging to the first and third age group, according to the definition in groups. For instance, list("FORM","ref") using the category name for categorical covariates.

• color (vector) - Vector of covariates used for coloring (by default no coloring is applied). For instance c("FORM","AGE").

• colors - Vector of colors to use when color argument is used. Takes precedence over colors defined in preferences. For instance c("#ebecf0","#cdced1","#97989c").

• individualSelection - Ids to display (by default the 12 first ids are displayed) defined as:

  • indices (vector) - Indices of the individuals to display (by default, the 12 first individuals are selected). If occasions are present, all occasions of the selected individuals will be displayed. Takes precedence over ids. For instance c(5,6,10,11).

  • isRange (logical) - If TRUE, all individuals whose index is inside [min(indices), max[indices]] are selected (FALSE by default). Forced to FALSE if ids is defined.

  • ids (vector) - Names of the individuals to display. If occasions are present, all occasions of the selected individuals will be displayed. For instance c("101-01","101-02","101-03"). If ids are integers, can also be c(1,3,6). Ignored if indices is defined.

preferences

(optional) preferences for plot display, run getPlotPreferences("plotBivariateDataViewer") to check available displays.

Value

A ggplot object

See also

Examples

R

  initializeLixoftConnectors(software = "monolix")
  project <- file.path(getDemoPath(), "1.creating_and_using_models",
                       "1.1.libraries_of_models", "warfarinPKPD_project.mlxtran")
  loadProject(project)

  plotBivariateDataViewer(obs1 = "y1", obs2 = "y2")

R

  plotBivariateDataViewer(settings = list(lines = FALSE))
#> Warning: obs1 not specified. It is set to y1.
#> Warning: obs2 not specified. It is set to y2.

R

  # stratification
  plotBivariateDataViewer(obs1 = "y1", obs2 = "y2", stratify = list(individualSelection = list(indices = 10)))

R

  plotBivariateDataViewer(stratify = list(split = "age",
                                          filter = list("sex", "1"),
                                          groups = list(name = "age", definition = c(25))))
#> Warning: obs1 not specified. It is set to y1.
#> Warning: obs2 not specified. It is set to y2.

R

  plotBivariateDataViewer(stratify = list(color = "wt",
                                          groups = list(name = "wt", definition = 75)))
#> Warning: obs1 not specified. It is set to y1.
#> Warning: obs2 not specified. It is set to y2.

R

  plotBivariateDataViewer(stratify = list(split = c("age", "sex"),
                                          groups = list(name = "age", definition = 25)))
#> Warning: obs1 not specified. It is set to y1.
#> Warning: obs2 not specified. It is set to y2.

R

  # update plot settings or preferences
  plotBivariateDataViewer(preferences = list(obs = list(color = "#32CD32")))
#> Warning: obs1 not specified. It is set to y1.
#> Warning: obs2 not specified. It is set to y2.

R

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