plotDimReduceFeature: Plotting feature expression on a dimension reduction plot
In campbio/celda: CEllular Latent Dirichlet Allocation

plotDimReduceFeature

R Documentation

Plotting feature expression 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 expression of the specified feature.

Usage

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 signature '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 signature '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)

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