markerExpressionPerCluster {scDataviz} | R Documentation

## Generate box-and-whisker plots illustrating marker expression per k-NN identified cluster. By default, 5 randomly-selected clusters are selected, and the expression profiles of 10 randomly-selected markers are plot across these.

### Description

Generate box-and-whisker plots illustrating marker expression per k-NN identified cluster. By default, 5 randomly-selected clusters are selected, and the expression profiles of 10 randomly-selected markers are plot across these.

### Usage

    markerExpressionPerCluster(
      indata,
      assay = "scaled",
      clusters = sample(unique(metadata(indata)[["Cluster"]]), 5),
      clusterAssign = metadata(indata)[["Cluster"]],
      markers = sample(rownames(indata), 10),
      ncol = 5,
      nrow = 2,
      legendPosition = "none",
      legendLabSize = 12,
      legendKeyHeight = 2.5,
      xlim = NULL,
      ylim = NULL,
      yfixed = FALSE,
      xlab = "Marker",
      xlabAngle = 90,
      xlabhjust = 0.5,
      xlabvjust = 0.5,
      ylab = "Expression",
      ylabAngle = 0,
      ylabhjust = 0.5,
      ylabvjust = 0.5,
      axisLabSize = 16,
      stripLabSize = 16,
      title = "Marker expression per cluster",
      subtitle = "",
      caption = "",
      titleLabSize = 16,
      subtitleLabSize = 12,
      captionLabSize = 12,
      borderWidth = 0.8,
      borderColour = "black",
      verbose = TRUE
    )

### Arguments

`indata` | A data-frame or matrix, or SingleCellExperiment object. If a data-frame or matrix, this should relate to expression data (cells as columns; genes as rows). If a `SingleCellExperiment` object, data will be extracted from an assay component named by `assay`.
`assay` | Name of the assay slot in `indata` from which data will be taken, assuming `indata` is a `SingleCellExperiment` object.
`clusters` | Vector containing clusters to plot.
`clusterAssign` | A vector of cell-to-cluster assignments. This can be from any source but must align with your cells / variables. There is no check to ensure this when `indata` is not a `SingleCellExperiment` object.
`markers` | Vector containing marker names to plot.
`ncol` | Number of columns for faceting.
`nrow` | Number of rows for faceting.
`legendPosition` | Position of legend `('top', 'bottom', 'left', 'right', 'none')`.
`legendLabSize` | Size of plot legend text.
`legendKeyHeight` | Height of the legend key.
`xlim` | Limits of the x-axis.
`ylim` | Limits of the y-axis.
`yfixed` | Logical, specifying whether or not to fix the y-axis scales across all clusters when faceting.
`xlab` | Label for x-axis.
`xlabAngle` | Rotation angle of x-axis labels.
`xlabhjust` | Horizontal adjustment of x-axis labels.
`xlabvjust` | Vertical adjustment of x-axis labels.
`ylab` | Label for y-axis.
`ylabAngle` | Rotation angle of y-axis labels.
`ylabhjust` | Horizontal adjustment of y-axis labels.
`ylabvjust` | Vertical adjustment of y-axis labels.
`axisLabSize` | Size of x- and y-axis labels.
`stripLabSize` | Size of the strip labels.
`title` | Plot title.
`subtitle` | Plot subtitle.
`caption` | Plot caption.
`titleLabSize` | Size of plot title.
`subtitleLabSize` | Size of plot subtitle.
`captionLabSize` | Size of plot caption.
`borderWidth` | Width of the border on the x and y axes.
`borderColour` | Colour of the border on the x and y axes.
`verbose` | Boolean (TRUE / FALSE) to print messages to console or not.

### Details

Generate box-and-whisker plots illustrating marker expression per k-NN identified cluster. By default, 5 randomly-selected clusters are selected, and the expression profiles of 10 randomly-selected markers are plot across these.

### Value

A `ggplot2` object.

### Author(s)

Kevin Blighe <kevin@clinicalbioinformatics.co.uk>

### Examples

    # create random data that follows a negative binomial
    mat <- jitter(matrix(
      MASS::rnegbin(rexp(5000, rate=.1), theta = 4.5),
      ncol = 20))
    colnames(mat) <- paste0('CD', 1:ncol(mat))
    rownames(mat) <- paste0('cell', 1:nrow(mat))

    clus <- clusKNN(mat)
    markerExpressionPerCluster(t(mat), clusters = c(0, 1),
      clusterAssign = clus)

[Package scDataviz version 1.0.0 Index]