Plotting feature expression 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 expression of the specified feature.

plotDimReduceFeature(
  x,
  features,
  reducedDimName = NULL,
  displayName = NULL,
  dim1 = NULL,
  dim2 = NULL,
  headers = NULL,
  useAssay = "counts",
  altExpName = "featureSubset",
  normalize = FALSE,
  zscore = TRUE,
  exactMatch = TRUE,
  trim = c(-2, 2),
  limits = c(-2, 2),
  size = 0.5,
  xlab = NULL,
  ylab = NULL,
  colorLow = "blue4",
  colorMid = "grey90",
  colorHigh = "firebrick1",
  midpoint = 0,
  ncol = NULL,
  decreasing = FALSE
)

# S4 method for SingleCellExperiment
plotDimReduceFeature(
  x,
  features,
  reducedDimName = NULL,
  displayName = NULL,
  dim1 = 1,
  dim2 = 2,
  headers = NULL,
  useAssay = "counts",
  altExpName = "featureSubset",
  normalize = FALSE,
  zscore = TRUE,
  exactMatch = TRUE,
  trim = c(-2, 2),
  limits = c(-2, 2),
  size = 0.5,
  xlab = NULL,
  ylab = NULL,
  colorLow = "blue4",
  colorMid = "grey90",
  colorHigh = "firebrick1",
  midpoint = 0,
  ncol = NULL,
  decreasing = FALSE
)

# S4 method for ANY
plotDimReduceFeature(
  x,
  features,
  dim1,
  dim2,
  headers = NULL,
  normalize = FALSE,
  zscore = TRUE,
  exactMatch = TRUE,
  trim = c(-2, 2),
  limits = c(-2, 2),
  size = 0.5,
  xlab = "Dimension_1",
  ylab = "Dimension_2",
  colorLow = "blue4",
  colorMid = "grey90",
  colorHigh = "firebrick1",
  midpoint = 0,
  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.

features

Character vector. Features in the rownames of counts to plot.

reducedDimName

The name of the dimension reduction slot in reducedDimNames(x) if x is a SingleCellExperiment object. If NULL, then both dim1 and dim2 need to be set. Default NULL.

displayName

Character. The column name of rowData(x) that specifies the display names for the features. Default NULL, which displays the row names. Only works if x is a SingleCellExperiment object. Overwrites headers.

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.

headers

Character vector. If NULL, the corresponding rownames are used as labels. Otherwise, these headers are used to label the features. Only works if displayName is NULL and exactMatch is FALSE.

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".

normalize

Logical. Whether to normalize the columns of `counts`. Default FALSE.

zscore

Logical. Whether to scale each feature to have a mean 0 and standard deviation of 1. Default TRUE.

exactMatch

Logical. Whether an exact match or a partial match using grep() is used to look up the feature in the rownames of the counts matrix. Default TRUE.

trim

Numeric vector. Vector of length two that specifies the lower and upper bounds for the data. This threshold is applied after row scaling. Set to NULL to disable. Default c(-1,1).

limits

Passed to scale_colour_gradient2. The range of color scale.

size

Numeric. Sets size of point on plot. Default 1.

xlab

Character vector. Label for the x-axis. If reducedDimName is used, then this will be set to the column name of the first dimension of that object. Default "Dimension_1".

ylab

Character vector. Label for the y-axis. If reducedDimName is used, then this will be set to the column name of the second dimension of that object. Default "Dimension_2".

colorLow

Character. A color available from `colors()`. The color will be used to signify the lowest values on the scale.

colorMid

Character. A color available from `colors()`. The color will be used to signify the midpoint on the scale.

colorHigh

Character. A color available from `colors()`. The color will be used to signify the highest values on the scale.

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.

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)
plotDimReduceFeature(x = sce,
  reducedDimName = "celda_tSNE",
  normalize = TRUE,
  features = c("Gene_98", "Gene_99"),
  exactMatch = TRUE)

library(SingleCellExperiment)
data(sceCeldaCG)
sce <- celdaTsne(sceCeldaCG)
plotDimReduceFeature(x = counts(sce),
  dim1 = reducedDim(altExp(sce), "celda_tSNE")[, 1],
  dim2 = reducedDim(altExp(sce), "celda_tSNE")[, 2],
  normalize = TRUE,
  features = c("Gene_98", "Gene_99"),
  exactMatch = TRUE)