plotSCEDimReduceFeatures {singleCellTK} | R Documentation

## Dimension reduction plot tool for assay data

### Description

Plot results of reduced dimensions data and colors by feature data stored in the assays slot.

### Usage

    plotSCEDimReduceFeatures(
      inSCE,
      sample = NULL,
      feature,
      shape = NULL,
      reducedDimName,
      useAssay = "logcounts",
      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,
      legendTitle = NULL,
      legendSize = 10,
      legendTitleSize = 12,
      groupBy = NULL,
      combinePlot = "none",
      plotLabels = NULL
    )

### Arguments

`inSCE` | Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required
`sample` | Character vector. Indicates which sample each cell belongs to.
`feature` | name of feature stored in assay of singleCellExperiment object. Plot will be colored based on feature value.
`shape` | add shapes to each condition. Default NULL.
`reducedDimName` | saved dimension reduction name in the SingleCellExperiment object. Required.
`useAssay` | Indicate which assay to use. The default is "logcounts"
`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.
`legendTitle` | title of legend. Default NULL.
`legendSize` | size of legend. Default 10.
`legendTitleSize` | size of legend title. Default 12.
`groupBy` | Facet wrap the scatterplot based on value. Default `NULL`.
`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 dimension plot of feature data.

### Examples

    plotSCEDimReduceFeatures(
      inSCE = mouseBrainSubsetSCE, feature = "Apoe",
      shape = NULL, reducedDimName = "TSNE_counts",
      useAssay = "counts", xlab = "tSNE1", ylab = "tSNE2"
    )

[Package singleCellTK version 2.0.0 Index]