R: Arrange bubbleHeatmap Arguments in Lists for Building...

multiPlotInput {bubbleHeatmap}

R Documentation

Arrange bubbleHeatmap Arguments in Lists for Building Multiple Plots.

Description

Build bubbleHeatmap arguments into a list of lists to facilitate building of multiple plots in a single call. It is useful for creating sets of plots with the same data scales, similar plots with minor differences in settings, or the supplied Nightingale plot template.

Usage

multiPlotInput(
  colorList,
  sizeList = colorList,
  nightingale = TRUE,
  treeNames = names(colorList),
  context = gpar(cex = 0.8),
  colorSeq = c("#053061", "#2166AC", "#4393C3", "#92C5DE", "#D1E5F0", "#FDDBC7",
    "#F4A582", "#D6604D", "#B2182B", "#67001F"),
  unitBase = unit(0.5, "cm"),
  diameter = 0.8,
  colorLim = c(NA, NA),
  sizeLim = c(NA, NA),
  showTopLabels = TRUE,
  showLeftLabels = TRUE,
  leftLabelsTitles = FALSE,
  showRowBracket = FALSE,
  rowTitles = FALSE,
  showColBracket = FALSE,
  colTitles = FALSE,
  plotTitles = FALSE,
  xTitles = FALSE,
  yTitles = FALSE,
  showColorLegend = TRUE,
  showBubbleLegend = TRUE,
  colorBreaks = NULL,
  sizeBreaks = NULL,
  legendHeight = nrow(colorList[[1]]),
  legendTitles = c(expression("-log"[10] * "P"), "Estimate (SD)")
)

Arguments

`colorList`, `sizeList`	List of matrices, each item representing one plot, containing values to be plotted as the bubble color and size respectively. If `sizeList` is not supplied then color values will also be used for size.
`nightingale`	Logical, apply Nightingale style template?
`treeNames`	Vector of names for gTrees output by bubbleHeatmap, if not supplied then `names(colorList)` will be used.
`context`	`gpar` object to provide drawing context. Will be applied to the parent viewport in the childrenvp slot of gTrees output by bubbleHeatmap.
`colorSeq`	Vector of colors to distribute over color scale gradient.
`unitBase`	`unit` object indicating the size of one plot grid square.
`diameter`	Maximum diameter of bubbles as multiple of unitBase.
`colorLim`, `sizeLim`	Numeric vectors indicating limits (min/max) beyond which the values of color/size matrices should be truncated.
`showTopLabels`	Logical vector, should matrix column names be printed above each plot? Should have `length == length(colorList)` or `length == 1` to use same value for all plots.
`showLeftLabels`	Logical vector, should matrix row names be printed above each plot? Should have `length == length(colorList)` or `length == 1` to use same value for all plots.
`leftLabelsTitles`	Vector of headings to go over the row names of each plot. Character strings or FALSE for no title. A single FALSE value can also be used if no left label titles are required.
`showRowBracket`	Logical vector, should vertical bracket be printed to the right of each plot (to label a row of plots in a final figure layout)? Should have `length == length(colorList)` or `length == 1` to use same value for all plots.
`rowTitles`	Vector of labels to be printed to the right of each plot, outside row bracket if present (to label a row of plots in a final figure layout). Character strings or FALSE for no title. A single FALSE value can also be used if no row titles are required.
`showColBracket`	Logical vector, should horizontal bracket be printed below each plot (to label a column of plots in a final figure layout)? Should have `length == length(colorList)` or `length == 1` to use same value for all plots.
`colTitles`	Vector of labels to be printed to the right of each plot, outside col bracket if present (to label a column of plots in a final figure layout). Character strings or FALSE for no title. A single FALSE value can also be used if no column titles are required.
`plotTitles`	Vector of plot titles to be centered above each plot. Character strings or FALSE for no title. A single FALSE value can also be used if no plot titles are required.
`xTitles`	Vector of x axis titles to be printed left of `LeftLabels`. Character strings or FALSE for no title. A single FALSE value can also be used if no x axis titles are required.
`yTitles`	Vector of y axis titles to be printed above `TopLabels`. Character strings or FALSE for no title. A single FALSE value can also be used if no y axis titles are required.
`showColorLegend`, `showBubbleLegend`	Logicals, should a legend be produced for color scale/bubble size? If vector with `length == length(colorList)` then values will be input for each plot and any legends produced will be an element of a plot tree. A single TRUE value will build the legends outside the plots as separate trees.
`colorBreaks`, `sizeBreaks`	Character vectors of legend tick labels. If not supplied then these will be generated using pretty to a range outside data values (after values truncated to `colorLim`\`sizeLim` if applicable).
`legendHeight`	Numeric, preferred height of legends as multiple of `unitBase`. This will be supplied to pretty function. If sizeBreaks is supplied then this will be ignored and legend height will be `length(sizeBreaks)`.
`legendTitles`	Character vector of legend titles. First string should be the size legend title, second for the color legend.

Value

List with two elements:

trees: List of lists, arguments for bubbleHeatmap
legend: List of arguments for bubbleHMLegends

The list returned by this plot can be passed directly to bubbleHeatmapList to produce a list of plot trees.

Nightingale