Plotting the cell labels on a dimension reduction plot

Source: R/plot_dr.R

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.

plotDimReduceCluster(
  x,
  reducedDimName,
  altExpName = "featureSubset",
  dim1 = NULL,
  dim2 = NULL,
  size = 0.5,
  xlab = NULL,
  ylab = NULL,
  specificClusters = NULL,
  labelClusters = FALSE,
  groupBy = NULL,
  labelSize = 3.5
)

# S4 method for SingleCellExperiment
plotDimReduceCluster(
  x,
  reducedDimName,
  altExpName = "featureSubset",
  dim1 = 1,
  dim2 = 2,
  size = 0.5,
  xlab = NULL,
  ylab = NULL,
  specificClusters = NULL,
  labelClusters = FALSE,
  groupBy = NULL,
  labelSize = 3.5
)

# S4 method for vector
plotDimReduceCluster(
  x,
  dim1,
  dim2,
  size = 0.5,
  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

Integer or numeric vector. If reducedDimName is supplied, then, this will be used as an index to determine which dimension will be plotted on the x-axis. If reducedDimName is not supplied, then this should be a vector which will be plotted on the x-axis. Default 1.

dim2

Integer or numeric vector. If reducedDimName is supplied, then, this will be used as an index to determine which dimension will be plotted on the y-axis. If reducedDimName is not supplied, then this should be a vector which will be plotted on the y-axis. Default 2.

size

Numeric. Sets size of point on plot. Default 0.5.

xlab

Character vector. Label for the x-axis. Default NULL.

ylab

Character vector. Label for the y-axis. Default NULL.

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))