patientProfilesVis-common-args: Arguments used across the functions of the patientProfilesVis...
In patientProfilesVis: Visualization of Patient Profiles

patientProfilesVis-common-args

R Documentation

Arguments used across the functions of the patientProfilesVis package.

Description

Arguments used across the functions of the patientProfilesVis package.

Arguments

`data`	Data.frame with data.
`colorVar`	String, variable of `data` with color.
`colorLab`	String, label for `colorVar`.
`colorPalette`	Named vector with color palette. The variable should be named with the corresponding element in `colorVar`. Colors can also be defined for the entire session, by setting `options(patientProfilesVis.colors = X)` with X either: a vector with colors a function returning a vector of colors for a specified number of elements (`viridis` by default)
`shapeVar`	String, variable of `data` for shape of the points. By default, same as `colorVar`.
`shapeLab`	String, label for `shapeVar`. Set by default to `colorLab` if `colorVar` but not `shapeVar` is not specified.
`shapePalette`	Named character vector with shape palette for `shapeVar`. The variable should be named with the corresponding element in `shapeVar`. Shapes can also be defined for the entire session, by setting `options(patientProfilesVis.shapes = X)` with X either: a vector with shapes a function returning a vector of shapes for a specified number of elements Note it is advised to specify the shapes as character, e.g. 'cross' instead of `4`, in case Unicode symbols should also be used.
`paramGroupVar`	(optional) Character vector with variable(s) of `data` based on which the data will be grouped and sorted (in the y-axis) in the plot.
`xLab`	String, label for the x-axis.
`yLab`	String, label for the y-axis.
`label`	String, label for the visualization. This label is stored as attributes of the output from the `subjectProfile[]Plot` function. This label is displayed in the final profile report, in case no data is available for for a specific patient, as: 'No [label] available.'
`title`	String, title for the plot.
`timeVar`	String, variable of `data` with time, displayed in the x axis. Records with missing time are not displayed in the plot.
`timeLab`	String, label for `timeVar`. This is used in the message indicating missing values for `timeVar`, and for the default label of the x-axis.
`paramVar`	Character vector with variable(s) of `data` with parameters. Variable content is displayed in the y-axis.
`paramLab`	Named character vector, with label for the parameter variable(s) (`paramVar`). This is used to set the default title.
`timeLim`	(optional) Vector of length 2 with time limits (x-axis). If not specified, these are extracted from the minimum `timeStartVar` and maximum `timeEndVar` per subject. The time limits are stored as attributes of the plots, used to align the plots in the final report.
`timeTrans`	transformation for the time variable, (see `trans` parameter in `scale_x_continuous`, and `trans_new`). For example, produced by the `getTimeTrans` function.
`timeExpand`	Vector of range expansion constants for the time axis (see `expand` parameter in `scale_x_continuous`).
`listPlots`	Named list of subject profiles. Each sublist contains subject profiles as returned by the `subjectProfile[X]Plot` function, so nested by subject and page. The names of the list should be unique, and are used
`alpha`	Numeric with transparency, 1 by default.
`labelVars`	Named character vector with variable labels (names are the variable code)
`subjectVar`	String, variable of `data` with subject ID
`formatReport`	list with parameters used to specify the format of the report, e.g. output of the `subjectProfileReportFormat` function
`paramVarSep`	string with character(s) used to concatenate multiple `paramVar`, ' - ' by default.