Plotting Celda module probability on a dimension reduction plot

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 the module probability.

plotDimReduceModule(
  x,
  reducedDimName,
  useAssay = "counts",
  altExpName = "featureSubset",
  celdaMod,
  modules = NULL,
  dim1 = NULL,
  dim2 = NULL,
  size = 0.5,
  xlab = NULL,
  ylab = NULL,
  rescale = TRUE,
  limits = c(0, 1),
  colorLow = "grey90",
  colorHigh = "firebrick1",
  ncol = NULL,
  decreasing = FALSE
)

# S4 method for SingleCellExperiment
plotDimReduceModule(
  x,
  reducedDimName,
  useAssay = "counts",
  altExpName = "featureSubset",
  modules = NULL,
  dim1 = 1,
  dim2 = 2,
  size = 0.5,
  xlab = NULL,
  ylab = NULL,
  rescale = TRUE,
  limits = c(0, 1),
  colorLow = "grey90",
  colorHigh = "firebrick1",
  ncol = NULL,
  decreasing = FALSE
)

# S4 method for ANY
plotDimReduceModule(
  x,
  celdaMod,
  modules = NULL,
  dim1,
  dim2,
  size = 0.5,
  xlab = "Dimension_1",
  ylab = "Dimension_2",
  rescale = TRUE,
  limits = c(0, 1),
  colorLow = "grey90",
  colorHigh = "firebrick1",
  ncol = NULL,
  decreasing = FALSE
)

Arguments

x	Numeric matrix or a SingleCellExperiment object with the matrix located in the assay slot under useAssay. Rows represent features and columns represent cells.
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.
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".
celdaMod	Celda object of class "celda_G" or "celda_CG". Used only if x is a matrix object.
modules	Character vector. Module(s) from celda model to be plotted. e.g. c("1", "2").
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 "Dimension_1".
ylab	Character vector. Label for the y-axis. Default "Dimension_2".
rescale	Logical. Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE.
limits	Passed to scale_colour_gradient. 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.
colorHigh	Character. A color available from `colors()`. The color will be used to signify the highest values on the scale.
ncol	Integer. Passed to facet_wrap. Specify the number of columns for facet wrap.
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)
plotDimReduceModule(x = sce,
  reducedDimName = "celda_tSNE",
  modules = c("1", "2"))
library(SingleCellExperiment)
data(sceCeldaCG, celdaCGMod)
sce <- celdaTsne(sceCeldaCG)
plotDimReduceModule(x = counts(sce),
  dim1 = reducedDim(altExp(sce), "celda_tSNE")[, 1],
  dim2 = reducedDim(altExp(sce), "celda_tSNE")[, 2],
  celdaMod = celdaCGMod,
  modules = c("1", "2"))