Plotting Celda module probability 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 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"))