esetPlotWrapper: wrapper for biplot of features/samples contained in a eSet...
In esetVis: Visualizations of expressionSet Bioconductor object

Description Usage Arguments Value Author(s) Examples

Wrapper function used for all plots of the visualizations contained in the package.

esetPlotWrapper(dataPlotSamples, dataPlotGenes = data.frame(), esetUsed,
  xlab = "", ylab = "", colorVar = character(0), color = if
  (length(colorVar) == 0) "black" else character(0),
  shapeVar = character(0), shape = if (length(shapeVar) == 0) 15 else
  numeric(0), sizeVar = character(0), size = if (length(sizeVar) == 0)
  {     ifelse(typePlot == "interactive" && length(packageInteractivity) ==
  1 && packageInteractivity == "rbokeh", 5, 2.5) } else {     numeric() },
  sizeRange = numeric(0), alphaVar = character(0), alpha = if
  (length(alphaVar) == 0) 1 else numeric(0), alphaRange = numeric(0),
  title = "", symmetryAxes = c("combine", "separate", "none"),
  cloudGenes = TRUE, cloudGenesColor = "black", cloudGenesNBins = if
  (nrow(dataPlotGenes) > 0) sqrt(nrow(dataPlotGenes)) else numeric(),
  cloudGenesIncludeLegend = FALSE, cloudGenesTitleLegend = "nGenes",
  packageTextLabel = c("ggrepel", "ggplot2"), topGenes = 10,
  topGenesCex = 2.5, topGenesVar = character(0),
  topGenesJust = c(0.5, 0.5), topGenesColor = "black",
  topSamples = 10, topSamplesCex = 2.5, topSamplesVar = character(0),
  topSamplesJust = c(0.5, 0.5), topSamplesColor = "black",
  geneSets = list(), geneSetsVar = character(0),
  geneSetsMaxNChar = numeric(0), topGeneSets = 10,
  topGeneSetsCex = 2.5, topGeneSetsJust = c(0.5, 0.5),
  topGeneSetsColor = "black", includeLegend = TRUE,
  includeLineOrigin = TRUE, typePlot = c("static", "interactive"),
  figInteractiveSize = c(600, 400), ggvisAdjustLegend = TRUE,
  interactiveTooltip = TRUE,
  interactiveTooltipExtraVars = character(0),
  packageInteractivity = c("rbokeh", "ggvis"),
  returnTopElements = FALSE, returnEsetPlot = FALSE)

`dataPlotSamples`	data.frame with columns 'X', 'Y' with coordinates for the samples and with rownames which should correspond and be in the same order as the sampleNames of `esetUsed`
`dataPlotGenes`	data.frame with two columns 'X' and 'Y' with coordinates for the genes
`esetUsed`	expressionSet (or SummarizedExperiment) object with data
`xlab`	label for the x axis
`ylab`	label for the y axis
`colorVar`	name of variable (in varLabels of the `eset`) used for coloring, empty by default
`color`	character or factor with specified color(s) for the points, replicated if needed. This is used only if `colorVar` is empty. By default: 'black' if `colorVar` is not specified and default `ggplot` palette otherwise
`shapeVar`	name of variable (in varLabels of the `eset`) used for the shape, empty by default
`shape`	character or factor with specified shape(s) (pch) for the points, replicated if needed. This is used only if `shapeVar` is empty. By default: '15' (filled square) if `shapeVar` is not specified and default `ggplot` shape(s) otherwise
`sizeVar`	name of variable (in varLabels of the `eset`) used for the size, empty by default
`size`	character or factor with specified size(s) (cex) for the points, replicated if needed. This is used only if `sizeVar` is empty. By default: '2.5' if `sizeVar` is not specified and default `ggplot` size(s) otherwise
`sizeRange,`	size (cex) range used in the plot, possible only if the `sizeVar` is 'numeric' or 'integer'
`alphaVar`	name of variable (in varLabels of the `eset`) used for the transparency, empty by default. This parameter is currently only available for static plot and ggvis (only numeric in this case).
`alpha`	character or factor with specified transparency(s) for the points, replicated if needed. This is used only if `shapeVar` is empty. By default: '1' if `alphaVar` is not specified and default `ggplot` alpha otherwise This parameter is currently only available for static and ggvis.
`alphaRange`	transparency (alpha) range used in the plot, possible only if the `alphaVar` is 'numeric' or 'integer' This parameter is currently only available for static and ggvis plot.
`title`	plot title, ” by default
`symmetryAxes`	set symmetry for axes, either: 'combine' (by default): both axes are symmetric and with the same limits 'separate': each axis is symmetric and has its own limits 'none': axes by default (plot limits)
`cloudGenes`	logical, if TRUE (by default), include the cloud of genes in the plot
`cloudGenesColor`	if `cloudGenes` is TRUE, color for the cloud of genes, black by default
`cloudGenesNBins`	number of bins to used for the clouds of genes, by default the square root of the number of genes
`cloudGenesIncludeLegend`	logical, if TRUE (FALSE by default) include the legend for the cloud of genes (in the top position if multiple legends)
`cloudGenesTitleLegend`	string with title for the legend for the cloud of genes 'nGenes' by default
`packageTextLabel`	package used to label the outlying genes/samples/gene sets, either `ggrepel` (by default, only used if package `ggrepel` is available), or `ggplot2`
`topGenes`	numeric indicating which percentile (if <1) or number (if >=1) of genes most distant to the origin of the plot to annotate, by default: 10 genes are selected If no genes should be annotated, set this parameter to 0 Currently only available for static plot.
`topGenesCex`	cex for gene annotation (used when `topGenes` > 0)
`topGenesVar`	variable of the featureData used to label the genes, by default: empty, the featureNames are used for labelling (used when `topGenes` > 0)
`topGenesJust`	text justification for the genes (used when `topGenes` > 0 and if `packageTextLabel` is `ggplot2`), by default: c(0.5, 0.5) so centered
`topGenesColor`	text color for the genes (used when `topGenes` > 0), black by default
`topSamples`	numeric indicating which percentile (if <1) or number (if >=1) of samples most distant to the origin of the plot to annotate, by default: 10 samples are selected If no samples should be annotated, set this parameter to 0. Currently available for static plot.
`topSamplesCex`	cex for sample annotation (used when `topSamples` > 0)
`topSamplesVar`	variable of the phenoData used to label the samples, by default: empty, the sampleNames are used for labelling (used when `topSample`s > 0)
`topSamplesJust`	text justification for the samples (used when `topSamples` > 0 and if `packageTextLabel` is `ggplot2`), by default: c(0.5, 0.5) so centered
`topSamplesColor`	text color for the samples (used when `topSamples` > 0), black by default
`geneSets`	list of gene sets/pathways, each containing identifiers of genes contained in the set. E.g. pathways from Gene Ontology databases output from the `getGeneSetsForPlot` function or any custom list of pathways. The genes identifiers should correspond to the variable `geneSetsVar` contained in the phenoData, if not specified the featureNames are used. If several gene sets have the same name, they will be combine to extract the top gene sets.
`geneSetsVar`	variable of the featureData used to match the genes contained in geneSets, most probably ENTREZID, if not specified the featureNames of the eSet are used Only used when `topGeneSets` > 0 and the parameter geneSets is specified.
`geneSetsMaxNChar`	maximum number of characters for pathway names, by default keep entire names Only used when `topGeneSets` > 0 and the parameter `geneSets` is specified. If `returnAnalysis` is set to TRUE and `geneSetsMaxNChar` specified, the top pathways will be returned in the output object, named with the identifiers used in the plot (so with maximum `geneSetsMaxNChar` number of characters)
`topGeneSets`	numeric indicating which percentile (if <=1) or number (if >1) of gene sets most distant to the origin of the plot to annotate, by default: 10 gene sets are selected If no gene sets should be annotated, set this parameter to 0. Currently available for static plot. Only used when `topGeneSets` > 0 and the parameter geneSets is specified.
`topGeneSetsCex`	cex for gene sets annotation Only used when `topGeneSets` > 0 and the parameter geneSets is specified.
`topGeneSetsJust`	text justification for the gene sets by default: c(0.5, 0.5) so centered Only used when `topGeneSets` > 0, the parameter `geneSets` is specified and if `packageTextLabel` is `ggplot2`.
`topGeneSetsColor`	color for the gene sets (used when `topGeneSets` > 0 and `geneSets` is specified), black by default Only used when `topGeneSets` > 0 and the parameter geneSets is specified.
`includeLegend`	logical if TRUE (by default) include a legend, otherwise not
`includeLineOrigin`	if TRUE (by default) include vertical line at x = 0 and horizontal line at y = 0
`typePlot`	type of the plot returned, either 'static' (static) or interactive' (potentially interactive)
`figInteractiveSize`	vector containing the size of the interactive plot, as [width, height] by default: c(600, 400). This is passed to the `width` and `height` parameters of: for rbokeh plots: the `bokeh::figure` function for ggvis plots: the `ggvis::set_options` function
`ggvisAdjustLegend`	logical, if TRUE (by default) adjust the legends in `ggvis` to avoid overlapping legends when multiple legends
`interactiveTooltip`	logical, if TRUE, add hoover functionality showing sample annotation (variables used in the plot) in the plot
`interactiveTooltipExtraVars`	name of extra variable(s) (in varLabels of the `eset`) to add in rbokehEsetPlot to label the samples, empty by default
`packageInteractivity`	if `typePlot` is 'interactive', package used for interactive plot, either 'rbokeh' (by default) or 'ggvis'
`returnTopElements`	logical, if TRUE return also the top elements
`returnEsetPlot`	logical, if TRUE return also the esetPlot object

if typePlot is:

static:
- if returnTopElements is TRUE, and top elements can be displayed, a list with:
  - 'topElements': the top elements labelled in the plot
  - 'plot': the ggplot object
- otherwise, the ggplot object only
interactive: a ggvis or rbokeh object, depending on the packageInteractivity parameter

Laure Cougnaud

library(ALL)
data(ALL)

## run one spectral map analysis

# create custom color palette
colorPalette <- c("dodgerblue", colorRampPalette(c("white","dodgerblue2", "darkblue"))(5)[-1], 
	"red", colorRampPalette(c("white", "red3", "darkred"))(5)[-1])

# run the analysis
# with 'returnAnalysis' set to TRUE to have all objects required for the esetPlotWrapper
outputEsetSPM <- esetSpectralMap(eset = ALL, 
	title = "Acute lymphoblastic leukemia dataset \n Spectral map complete",
	colorVar = "BT", color = colorPalette,
	shapeVar = "sex", shape = 15:16,
	sizeVar = "age", sizeRange = c(2, 6),
	symmetryAxes = "separate",
	topGenes = 10, topGenesJust = c(1, 0), topGenesCex = 2, topGenesColor = "darkgrey",
	topSamples = 15, topSamplesVar = "cod", topSamplesColor = "black",
	topSamplesJust = c(1, 0), topSamplesCex = 3, returnAnalysis = TRUE)

# plot the biplot
print(outputEsetSPM$plot)


## re-call the plot function, to change some visualizations parameters
esetPlotWrapper(
	dataPlotSamples = outputEsetSPM$analysis$dataPlotSamples,
	dataPlotGenes = outputEsetSPM$analysis$dataPlotGenes,
	esetUsed = outputEsetSPM$analysis$esetUsed,
	title = paste("Acute lymphoblastic leukemia dataset \n Spectral map"),
	colorVar = "BT", color = colorPalette,
	shapeVar = "relapse", 
	sizeVar = "age", sizeRange = c(2, 6),
	topSamplesVar = "cod", topGenesVar = "SYMBOL"
)