esetPlot-class {esetVis} | R Documentation

## An S4 class to represent `esetPlot` object expressionSet with visualization data from dimension-reduction methods

### Description

Constructor of the esetPlot class

### Usage

    ## S4 method for signature 'esetPlot'
    initialize(.Object, ...)

### Arguments

`.Object` | esetPlot object
`...` | additional class arguments

### Value

S4 object of class `esetPlot`

### Slots

`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

`eset`

  expressionSet (or SummarizedExperiment) object with data

`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`

  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.

`alpha`

  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.

`alphaRange`

  transparency (alpha) range used in the plot, possible only if the `alphaVar` is 'numeric' or 'integer' This parameter is not available for rbokeh plot.

`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 spectral map

`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.

`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

[Package esetVis version 1.10.0 Index]