subjectProfileSummaryPlot: Plot subject summary profile.
In inTextSummaryTable: Creation of in-Text Summary Table

View source: R/subjectProfileSummaryPlot.R

subjectProfileSummaryPlot

R Documentation

Plot subject summary profile.

Description

The user can either specify a variable for the standard error (seVar), or directly the variables for the minimum and maximum values for the error bars (minVar, maxVar).

Usage

subjectProfileSummaryPlot(
  data,
  xVar = NULL,
  xLab = getLabelVar(xVar, labelVars = labelVars),
  xAxisExpand = waiver(),
  xGap = NULL,
  xGapDiffNew = NULL,
  meanVar = "statMean",
  seVar = if ("statSE" %in% colnames(data)) "statSE",
  minVar = NULL,
  maxVar = NULL,
  yLab = paste(c(sub("^stat", "", meanVar), if (!is.null(minVar) & !is.null(maxVar)) {
  
      paste0("(", sub("^stat", "", minVar), ", ", sub("^stat", "", maxVar), ")")
 } else
    if (!is.null(seVar)) paste("+-", sub("^stat", "", seVar))), collapse = " "),
  facetVar = NULL,
  facetScale = "free_y",
  colorVar = NULL,
  colorLab = getLabelVar(colorVar, labelVars = labelVars),
  colorPalette = NULL,
  labelVars = NULL,
  useLinetype = TRUE,
  linetypePalette = NULL,
  useShape = TRUE,
  shapePalette = NULL,
  jitter = NULL,
  title = NULL,
  caption = NULL,
  yTrans = NULL,
  yLim = NULL,
  xLim = NULL,
  yAxisExpand = c(0.05, 0.05),
  yLimExpand = NULL,
  xAxisLabs = NULL,
  sizePoint = GeomPoint$default_aes$size,
  sizeLine = GeomLine$default_aes$size,
  sizeLabel = GeomText$default_aes$size,
  widthErrorBar = GeomErrorbar$default_aes$width,
  tableText = NULL,
  tableTextFontface = 1,
  tableHeight = 0.1,
  tableYAxisLabs = !is.null(colorVar),
  tablePlotMargin = unit(0, "pt"),
  label = FALSE,
  labelPadding = unit(1, "lines"),
  byVar = NULL,
  hLine = NULL,
  hLineColor = "black",
  hLineLty = "solid",
  vLine = NULL,
  vLineColor = "black",
  vLineLty = "solid",
  style = "report",
  fontname = switch(style, report = "Times", presentation = "Tahoma"),
  fontsize = switch(style, report = 8, presentation = 10),
  themeFct = switch(style, report = theme_classic, presentation = theme_bw),
  themeIncludeVerticalGrid = TRUE,
  ggExtra = NULL,
  legendPosition = ifelse(!is.null(tableText), "none", "bottom"),
  ...
)

Arguments

`data`	Data.frame with summary statistics to represent in the plot, e.g. a `summaryTable` object.
`xVar`	String, variable of `data` with variable for the x-axis.
`xLab`	String with label for the `xVar`.
`xAxisExpand`	Object passed to the 'expand' parameter of: `scale_x_continuous`, (`waiver` by default).
`xGap`	(optional) Numeric vector of length 2 for which a gap should be created in the x-axis. Only available if `xVar` is specified and a numeric variable. Records with `xVar` within `xGap` are filtered from the plot, vertical lines are included at the min/max of the gap, and the gap is represented as '//' in the x-axis of the plot.
`xGapDiffNew`	Numeric vector of length 2 with new range of the `xGap`. If not specified, the minimum difference between consecutive x elements in the data is used.
`meanVar`	String, variable of `data` with the mean variable.
`seVar`	String, variable of `data` with the standard error.
`minVar, maxVar`	String, variables of `data` with minimum and maximum value for error bar. If both are specified, `seVar` is ignored.
`yLab`	String with label for the y-axis. If different labels should be used for different elements of `byVar` variable, the vector should be named with each corresponding element (collapsed with '.' if multiple).
`facetVar`	Character vector, variable(s) of `data` for facetting.
`facetScale`	String with type of scale used for facetting, 'free_y' by default (fixed scale in the x-axis and free in the y-axis).
`colorVar`	String, variable of `data` for coloring.
`colorLab`	String, label for `colorVar`, used in the legend.
`colorPalette`	(named) Vector with color palette.
`labelVars`	Named string with variable labels (names are the variable code).
`useLinetype`	Logical, if TRUE (FALSE by default) use also linetype to differenciate the variable specified via `colorVar` in the mean line.
`linetypePalette`	Vector with linetype(s), in case `useLinetype` is TRUE.
`useShape`	Logical, if TRUE (by default) `colorVar` is also used for the shape.
`shapePalette`	Named vector with shape palette for `colorVar`.
`jitter`	Numeric with jitter for the x-axis, only used if `colorVar` specified.
`title`	String with title for the plot. If different labels should be used for different elements of `byVar` variable, the vector should be named with each corresponding element (collapsed with '.' if multiple).
`caption`	String with caption for the plot, NULL by default.
`yTrans`	(optional) String with transformation for the y-axis. Currently only 'log10' (or NULL, default) is available. In case error bars go in the negative, their values are set to a 'small enough' value for plotting: `min(data)/10` or `yLim[1]` if `yLim` is specified.
`yLim`	Vector of the length 2 with limits for the y-axis.
`xLim`	Vector of the length 2 with limits for the x-axis.
`yAxisExpand`	Expansion constants for the limits for the y-axis. See the documentation of the `expand` parameter of the `scale_y_continuous` function for the available values for this parameter.
`yLimExpand`	This parameter is deprecated, use `yAxisExpand` instead.
`xAxisLabs`	(optional) Named character vector with labels for the x-axis.
`sizePoint`	Size for the point.
`sizeLine`	Size for the line linking means and error bars.
`sizeLabel`	Size for the label, only used if `label` is not NULL.
`widthErrorBar`	Numeric vector of length 1 with width of error bar.
`tableText`	(optional) Character vector with colname of `data` or expression from colnames of `data` to be represented in the table below the plot. By default, no table is displayed.
`tableTextFontface`	Font face for the text included in the table.
`tableHeight`	Numeric of length 1 with height for the table.
`tableYAxisLabs`	Logical, if TRUE (by default) the labels of the `colorVar` are included in the y-axis of the table.
`tablePlotMargin`	Margin between the plot and the table, expressed as `unit`, 0 by default.
`label`	Logical or expression or list of expression. Points are labelled with `meanVar` if set to TRUE, or with the specified expression if `label` is an expression. If a list is specified, 'textLabel' (required) should contain expression to extract label, and 'textHjust' and 'textVjust' (optional) may contain expression specifying horizontal and vertical adjustment of the label.
`labelPadding`	Amount of padding (space) between each point and its `label`, 1.5 lines by default. See parameter `point.padding` of the `geom_text_repel` function.
`byVar`	Variable(s) of `data` for which separated plot(s) should be created.
`hLine`	(optional) numeric with y-intercept of line(s) to be added. If different thresholds should be used for different elements of the `byVar` or `facetVar` variables, the vector should be named with each corresponding element (collapsed with '.' if multiple).
`hLineColor`	String with color for `hLine`, 'black' by default.
`hLineLty`	String with linetype for `hLine`, 'solid' by default.
`vLine`	(optional) numeric with x-intercept of line(s) to be added. If different thresholds should be used for different elements of the `byVar` or `facetVar` variables, the vector should be named with each corresponding element (collapsed with '.' if multiple).
`vLineColor`	String with color for `vLine`, 'black' by default.
`vLineLty`	String with linetype for `vLine`, 'solid' by defaul
`style`	String with subject profile style. This affects the parameters: `fontname`, `fontsize` and `themeFct`.
`fontname`	String with font name, by default 'Times' if `style` is 'report' and 'Tahoma' if `style` is 'presentation'.
`fontsize`	Numeric vector of length 1 with font size, by default 8 if `style` is 'report' and 10 if `style` is 'presentation'
`themeFct`	Function with ggplot2 theme, by default `theme_classic` if `style` is 'report' and `theme_bw` if `style` is 'presentation'.
`themeIncludeVerticalGrid`	Logical, if TRUE (by default) include theme vertical grid lines (if present in `themeFct`).
`ggExtra`	Extra `ggplot` call of function generating such call(s) to be added in main plot. Multiple calls are set via a function, e.g. `ggExtra = function(gg){gg + geom_vline(...) + geom_hline(...)}`. If different calls should be used for different elements of the `byVar` variable, the vector should be named with each corresponding element (collapsed with '.' if multiple).
`legendPosition`	String with legend position. By default, 'bottom' of `tableText` is not specified, 'none' otherwise.
`...`	Additional parameters for `geom_text_repel` or `geom_text` used for the `label`.