plotDimReduceGrid {celda} | R Documentation

## Mapping the dimension reduction plot

### Description

Creates a scatterplot given two dimensions from a data dimension reduction tool (e.g tSNE) output.

### Usage

    plotDimReduceGrid(
      x,
      reducedDimName,
      dim1 = NULL,
      dim2 = NULL,
      useAssay = "counts",
      altExpName = "featureSubset",
      size = 1,
      xlab = "Dimension_1",
      ylab = "Dimension_2",
      limits = c(-2, 2),
      colorLow = "blue4",
      colorMid = "grey90",
      colorHigh = "firebrick1",
      midpoint = 0,
      varLabel = NULL,
      ncol = NULL,
      headers = NULL,
      decreasing = FALSE
    )

    ## S4 method for signature 'SingleCellExperiment'
    plotDimReduceGrid(
      x,
      reducedDimName,
      dim1 = NULL,
      dim2 = NULL,
      useAssay = "counts",
      altExpName = "featureSubset",
      size = 1,
      xlab = "Dimension_1",
      ylab = "Dimension_2",
      limits = c(-2, 2),
      colorLow = "blue4",
      colorMid = "grey90",
      colorHigh = "firebrick1",
      midpoint = 0,
      varLabel = NULL,
      ncol = NULL,
      headers = NULL,
      decreasing = FALSE
    )

    ## S4 method for signature 'ANY'
    plotDimReduceGrid(
      x,
      dim1,
      dim2,
      size = 1,
      xlab = "Dimension_1",
      ylab = "Dimension_2",
      limits = c(-2, 2),
      colorLow = "blue4",
      colorMid = "grey90",
      colorHigh = "firebrick1",
      midpoint = 0,
      varLabel = NULL,
      ncol = NULL,
      headers = NULL,
      decreasing = FALSE
    )

### Arguments

`x` | Numeric matrix or a SingleCellExperiment object with the matrix located in the assay slot under `useAssay`. Each row of the matrix will be plotted as a separate facet.
`reducedDimName` | The name of the dimension reduction slot in `reducedDimNames(x)` if `x` is a SingleCellExperiment object. Ignored if both `dim1` and `dim2` are set.
`dim1` | Numeric vector. First dimension from data dimension reduction output.
`dim2` | Numeric vector. Second dimension from data dimension reduction output.
`useAssay` | A string specifying which assay slot to use if `x` is a SingleCellExperiment object. Default "counts".
`altExpName` | The name for the altExp slot to use. Default "featureSubset".
`size` | Numeric. Sets size of point on plot. Default 1.
`xlab` | Character vector. Label for the x-axis. Default 'Dimension_1'.
`ylab` | Character vector. Label for the y-axis. Default 'Dimension_2'.
`limits` | Passed to scale_colour_gradient2. The range of color scale.
`colorLow` | Character. A color available from 'colors()'. The color will be used to signify the lowest values on the scale. Default "blue4".
`colorMid` | Character. A color available from 'colors()'. The color will be used to signify the midpoint on the scale. Default "grey90".
`colorHigh` | Character. A color available from 'colors()'. The color will be used to signify the highest values on the scale. Default "firebrick1".
`midpoint` | Numeric. The value indicating the midpoint of the diverging color scheme. If `NULL`, defaults to the mean with 10 percent of values trimmed. Default `0`.
`varLabel` | Character vector. Title for the color legend.
`ncol` | Integer. Passed to facet_wrap. Specify the number of columns for facet wrap.
`headers` | Character vector. If 'NULL', the corresponding rownames are used as labels. Otherwise, these headers are used to label the genes.
`decreasing` | logical. Specifies the order of plotting the points. If `FALSE`, the points will be plotted in increasing order where the points with largest values will be on top. `TRUE` otherwise. If `NULL`, no sorting is performed. Points will be plotted in their current order in `x`. Default `FALSE`.

### Value

The plot as a ggplot object

### Examples

    data(sceCeldaCG)
    sce <- celdaTsne(sceCeldaCG)
    plotDimReduceGrid(x = sce,
      reducedDimName = "celda_tSNE",
      xlab = "Dimension1",
      ylab = "Dimension2",
      varLabel = "tSNE")
    library(SingleCellExperiment)
    data(sceCeldaCG)
    sce <- celdaTsne(sceCeldaCG)
    plotDimReduceGrid(x = counts(sce),
      dim1 = reducedDim(altExp(sce), "celda_tSNE")[, 1],
      dim2 = reducedDim(altExp(sce), "celda_tSNE")[, 2],
      xlab = "Dimension1",
      ylab = "Dimension2",
      varLabel = "tSNE")

[Package celda version 1.8.1 Index]