plotDimReduceCluster {celda} | R Documentation

## Plotting the cell labels on a dimension reduction plot

### Description

Create a scatterplot for each row of a normalized gene expression matrix where x and y axis are from a data dimension reduction tool. The cells are colored by "celda_cell_cluster" column in `colData(altExp(x, altExpName))` if `x` is a SingleCellExperiment object, or `x` if `x` is a integer vector of cell cluster labels.

### Usage

    plotDimReduceCluster(
      x,
      reducedDimName,
      altExpName = "featureSubset",
      dim1 = NULL,
      dim2 = NULL,
      size = 1,
      xlab = "Dimension_1",
      ylab = "Dimension_2",
      specificClusters = NULL,
      labelClusters = FALSE,
      groupBy = NULL,
      labelSize = 3.5
    )

    ## S4 method for signature 'SingleCellExperiment'
    plotDimReduceCluster(
      x,
      reducedDimName,
      altExpName = "featureSubset",
      dim1 = NULL,
      dim2 = NULL,
      size = 1,
      xlab = "Dimension_1",
      ylab = "Dimension_2",
      specificClusters = NULL,
      labelClusters = FALSE,
      groupBy = NULL,
      labelSize = 3.5
    )

    ## S4 method for signature 'vector'
    plotDimReduceCluster(
      x,
      dim1,
      dim2,
      size = 1,
      xlab = "Dimension_1",
      ylab = "Dimension_2",
      specificClusters = NULL,
      labelClusters = FALSE,
      groupBy = NULL,
      labelSize = 3.5
    )

### Arguments

`x` | Integer vector of cell cluster labels or a SingleCellExperiment object containing cluster labels for each cell in `"celda_cell_cluster"` column in `colData(x)`.
`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.
`altExpName` | The name for the altExp slot to use. Default "featureSubset".
`dim1` | Numeric vector. First dimension from data dimension reduction output.
`dim2` | Numeric vector. Second dimension from data dimension reduction output.
`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".
`specificClusters` | Numeric vector. Only color cells in the specified clusters. All other cells will be grey. If NULL, all clusters will be colored. Default `NULL`.
`labelClusters` | Logical. Whether the cluster labels are plotted. Default FALSE.
`groupBy` | Character vector. Contains sample labels for each cell. If NULL, all samples will be plotted together. Default NULL.
`labelSize` | Numeric. Sets size of label if labelClusters is TRUE. Default 3.5.

### Value

The plot as a ggplot object

### Examples

    data(sceCeldaCG)
    sce <- celdaTsne(sceCeldaCG)
    plotDimReduceCluster(x = sce,
      reducedDimName = "celda_tSNE",
      specificClusters = c(1, 2, 3))
    library(SingleCellExperiment)
    data(sceCeldaCG, celdaCGMod)
    sce <- celdaTsne(sceCeldaCG)
    plotDimReduceCluster(x = celdaClusters(celdaCGMod)$z,
      dim1 = reducedDim(altExp(sce), "celda_tSNE")[, 1],
      dim2 = reducedDim(altExp(sce), "celda_tSNE")[, 2],
      specificClusters = c(1, 2, 3))

[Package celda version 1.8.1 Index]