plotDimReduceGrid: Mapping the dimension reduction plot

In campbio/celda: CEllular Latent Dirichlet Allocation

Mapping the dimension reduction plot

Description

Creates a scatterplot given two dimensions from a data dimension reduction tool (e.g tSNE) output.

Usage

plotDimReduceGrid(
  x,
  reducedDimName,
  dim1 = NULL,
  dim2 = NULL,
  useAssay = "counts",
  altExpName = "featureSubset",
  size = 1,
  xlab = "Dimension_1",
  ylab = "Dimension_2",
  limits = c(-2, 2),
  colorLow = "blue4",
  colorMid = "grey90",
  colorHigh = "firebrick1",
  midpoint = 0,
  varLabel = NULL,
  ncol = NULL,
  headers = NULL,
  decreasing = FALSE
)

## S4 method for signature 'SingleCellExperiment'
plotDimReduceGrid(
  x,
  reducedDimName,
  dim1 = NULL,
  dim2 = NULL,
  useAssay = "counts",
  altExpName = "featureSubset",
  size = 1,
  xlab = "Dimension_1",
  ylab = "Dimension_2",
  limits = c(-2, 2),
  colorLow = "blue4",
  colorMid = "grey90",
  colorHigh = "firebrick1",
  midpoint = 0,
  varLabel = NULL,
  ncol = NULL,
  headers = NULL,
  decreasing = FALSE
)

## S4 method for signature 'ANY'
plotDimReduceGrid(
  x,
  dim1,
  dim2,
  size = 1,
  xlab = "Dimension_1",
  ylab = "Dimension_2",
  limits = c(-2, 2),
  colorLow = "blue4",
  colorMid = "grey90",
  colorHigh = "firebrick1",
  midpoint = 0,
  varLabel = NULL,
  ncol = NULL,
  headers = NULL,
  decreasing = FALSE
)

Arguments

x	Numeric matrix or a SingleCellExperiment object with the matrix located in the assay slot under useAssay. Each row of the matrix will be plotted as a separate facet.
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.
dim1	Numeric vector. Second dimension from data dimension reduction output.
dim2	Numeric vector. Second dimension from data dimension reduction output.
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".
size	Numeric. Sets size of point on plot. Default 1.
xlab	Character vector. Label for the x-axis. Default 'Dimension_1'.
ylab	Character vector. Label for the y-axis. Default 'Dimension_2'.
limits	Passed to scale_colour_gradient2. 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. Default "blue4".
colorMid	Character. A color available from 'colors()'. The color will be used to signify the midpoint on the scale. Default "grey90".
colorHigh	Character. A color available from 'colors()'. The color will be used to signify the highest values on the scale. Default "firebrick1".
midpoint	Numeric. The value indicating the midpoint of the diverging color scheme. If NULL, defaults to the mean with 10 percent of values trimmed. Default 0.
varLabel	Character vector. Title for the color legend.
ncol	Integer. Passed to facet_wrap. Specify the number of columns for facet wrap.
headers	Character vector. If 'NULL', the corresponding rownames are used as labels. Otherwise, these headers are used to label the genes.
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)
plotDimReduceGrid(x = sce,
  reducedDimName = "celda_tSNE",
  xlab = "Dimension1",
  ylab = "Dimension2",
  varLabel = "tSNE")
library(SingleCellExperiment)
data(sceCeldaCG)
sce <- celdaTsne(sceCeldaCG)
plotDimReduceGrid(x = counts(sce),
  dim1 = reducedDim(altExp(sce), "celda_tSNE")[, 1],
  dim2 = reducedDim(altExp(sce), "celda_tSNE")[, 2],
  xlab = "Dimension1",
  ylab = "Dimension2",
  varLabel = "tSNE")

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