clinDataReview-common-args {clinDataReview}

Common arguments for the functions of the clinDataReview package

Description

Common arguments for the functions of the clinDataReview package

Arguments

data

Data.frame with data.

verbose

Logical, if TRUE (FALSE by default) progress messages are printed in the current console. For the visualizations, progress messages during download of subject-specific report are displayed in the browser console.

gg

ggplot object.

pl

plotly object.

xVar

String with column of data containing x-variable.

yVar

String with column of data containing y-variable.

xLab

String with label for xVar.

xLabVar

(optional) Character vector with column(s) of data containing variable(s) to display in the label of the x-axis.

yLab

String with label for xVar.

yLabVar

(optional) Character vector with column(s) of data containing variable(s) to display in the label of the y-axis.

xLim, yLim

Numeric vector of length 2 with limits for the x/y axes.

idVar

String with variable containing subject ID.

idLab

String with label for idVar.

width

Numeric, width of the plot in pixels, 800 by default.

height

Numeric, height of the plot in pixels, 500 by default.

facetPars

List with facetting parameters, passed to the facetting function. Variables should be specified as character or formula. For 'wrap' facetting (facetType is 'wrap'), if the layout is not specified via nrow/ncol, 2 columns are used by default.

lineVars

List with parameters for the reference lines.

hoverVars

Character vector with variable(s) to be displayed in the hover, by default any position (and axis) and aesthetic variables displayed in the plot.

hoverLab

Named character vector with labels for hoverVars.

pathExpand

Logical, should the variable in pathExpand be included in a collapsible row or as hyperlink in the table? Should be TRUE for if multiple paths are included for each idVar, FALSE otherwise (by default).

table

Logical, if TRUE (FALSE by default) returns also a datatable containing the plot data. The plot and table are linked when included in a Rmarkdown document: when clicking on an plot element, only the corresponding records are retained in the associated table; when some records are selected in the table, they are highlighted in the associated table.

refLinePars

(optional) Nested list, with parameters for each reference line(s). Each sublist (a.k.a reference line) contains:

• aesthetic value(s) or variable(s) for the lines (in this case column names of data) for reference lines. The line position is controlled by the aesthetics supported in geom_vline, geom_hline and geom_abline.

• 'label': (optional) Logical specifying if the line should be annotated (FALSE to not annotate the line) or string with annotation label. By default, the value of the position of the horizontal/vertical line or the equation of the diagonal line is displayed.

labelVars

Named character vector containing variable labels.

id

String with general id for the plot:

• 'id' is used as group for the SharedData

• 'button:[id]' is used as button ID if table is TRUE

If not specified, a random id, as 'plotClinData[X]' is used.

title

String with title for the plot.

titleExtra

String with extra title for the plot (appended after title).

caption

String with caption.
The caption is included at the bottom right of the plot. Please note that this might overlap with vertical or rotated x-axis labels.

subtitle

String with subtitle.
The subtitle is included at the top left of the plot, below the title.

colorVar

(optional) String with color variable.

colorLab

String with label for colorVar.

colorPalette

(optional) Named character vector with color palette. If not specified, the viridis color palette is used.
See clinColors.

selectVars

(optional) Character vector with variable(s) from data for which a selection box should be included. This enables to select the data displayed in the plot (and associated table).

selectLab

(Named) character vector with label for selectVars.

keyVar

String with unique key variable, identifying unique group for which the link between the table and the plot should be done.

watermark

(optional) String with path to a file containing a watermark.

Value

No return value, used for the documentation of the functions of the package.