plotSCEScatter {singleCellTK} | R Documentation

## Dimension reduction plot tool for all types of data

### Description

Plot results of reduced dimensions data of counts stored in any slot in the SingleCellExperiment object.

### Usage

    plotSCEScatter(
      inSCE,
      slot = NULL,
      sample = NULL,
      annotation,
      feature = NULL,
      groupBy = NULL,
      shape = NULL,
      reducedDimName = NULL,
      conditionClass = NULL,
      xlab = NULL,
      ylab = NULL,
      axisSize = 10,
      axisLabelSize = 10,
      dim1 = NULL,
      dim2 = NULL,
      bin = NULL,
      binLabel = NULL,
      dotSize = 2,
      transparency = 1,
      colorLow = "white",
      colorMid = "gray",
      colorHigh = "blue",
      defaultTheme = TRUE,
      title = NULL,
      titleSize = 15,
      labelClusters = TRUE,
      legendTitle = NULL,
      legendTitleSize = 12,
      legendSize = 10,
      combinePlot = "none",
      plotLabels = NULL
    )

### Arguments

`inSCE` | Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required
`slot` | Desired slot of SingleCellExperiment used for plotting. Possible options: "assays", "colData", "metadata", "reducedDims". Default NULL.
`sample` | Character vector. Indicates which sample each cell belongs to.
`annotation` | Desired vector within the slot used for plotting. Default NULL.
`feature` | name of feature stored in assay of SingleCellExperiment object. Will be used only if "assays" slot is chosen. Default NULL.
`groupBy` | Group by a condition(any column of the annotation data). Default NULL.
`shape` | add shapes to each condition.
`reducedDimName` | saved dimension reduction name in the SingleCellExperiment object. Required.
`conditionClass` | class of the annotation data used in colorBy. Options are NULL, "factor" or "numeric". If NULL, class will default to the original class. Default NULL.
`xlab` | Character vector. Label for x-axis. Default NULL.
`ylab` | Character vector. Label for y-axis. Default NULL.
`axisSize` | Size of x/y-axis ticks. Default 10.
`axisLabelSize` | Size of x/y-axis labels. Default 10.
`dim1` | 1st dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.
`dim2` | 2nd dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL. Default is second PCA component for PCA data and NULL otherwise.
`bin` | Numeric vector. If single value, will divide the numeric values into the 'bin' groups. If more than one value, will bin numeric values using values as a cut point.
`binLabel` | Character vector. Labels for the bins created by the 'bin' parameter. Default NULL.
`dotSize` | Size of dots. Default 2.
`transparency` | Transparency of the dots, values will be 0-1. Default 1.
`colorLow` | Character. A color available from 'colors()'. The color will be used to signify the lowest values on the scale. Default 'white'.
`colorMid` | Character. A color available from 'colors()'. The color will be used to signify the midpoint on the scale. Default 'gray'.
`colorHigh` | Character. A color available from 'colors()'. The color will be used to signify the highest values on the scale. Default 'blue'.
`defaultTheme` | adds grid to plot when TRUE. Default TRUE.
`title` | Title of plot. Default NULL.
`titleSize` | Size of title of plot. Default 15.
`labelClusters` | Logical. Whether the cluster labels are plotted.
`legendTitle` | title of legend. Default NULL.
`legendTitleSize` | size of legend title. Default 12.
`legendSize` | size of legend. Default 10.
`combinePlot` | Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "none".
`plotLabels` | labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.

### Value

a ggplot of the reduced dimensions.

### Examples

    plotSCEScatter(
      inSCE = mouseBrainSubsetSCE, legendTitle = NULL,
      slot = "assays", annotation = "counts", feature = "Apoe",
      reducedDimName = "TSNE_counts", labelClusters = FALSE
    )

[Package singleCellTK version 2.0.0 Index]