plotDimReduceModule: Plotting Celda module probability on a dimension reduction...
In campbio/celda: CEllular Latent Dirichlet Allocation

plotDimReduceModule

R Documentation

Plotting Celda module probability 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 the module probability.

Usage

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 signature '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 signature '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"))

campbio/celda documentation built on April 5, 2024, 11:47 a.m.