Bar plot of assay data.

Visualizes values stored in the assay slot of a SingleCellExperiment object via a bar plot.

plotSCEBarAssayData(
  inSCE,
  feature,
  sample = NULL,
  useAssay = "counts",
  featureLocation = NULL,
  featureDisplay = NULL,
  groupBy = NULL,
  xlab = NULL,
  ylab = NULL,
  axisSize = 10,
  axisLabelSize = 10,
  dotSize = 0.1,
  transparency = 1,
  defaultTheme = TRUE,
  gridLine = FALSE,
  summary = NULL,
  title = NULL,
  titleSize = NULL,
  combinePlot = TRUE
)

Arguments

inSCE

Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

feature

Name of feature stored in assay of SingleCellExperiment object.

sample

Character vector. Indicates which sample each cell belongs to.

useAssay

Indicate which assay to use. Default "counts".

featureLocation

Indicates which column name of rowData to query gene.

featureDisplay

Indicates which column name of rowData to use to display feature for visualization.

groupBy

Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.

xlab

Character vector. Label for x-axis. Default NULL.

ylab

Character vector. Label for y-axis. Default NULL.

axisSize

Size of x/y-axis ticks. Default 10.

axisLabelSize

Size of x/y-axis labels. Default 10.

dotSize

Size of dots. Default 0.1.

transparency

Transparency of the dots, values will be 0-1. Default 1.

defaultTheme

Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

gridLine

Adds a horizontal grid line if TRUE. Will still be drawn even if defaultTheme is TRUE. Default FALSE.

summary

Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL.

title

Title of plot. Default NULL.

titleSize

Size of title of plot. Default 15.

combinePlot

Boolean. If multiple plots are generated (multiple samples, etc.), will combined plots using `cowplot::plot_grid`. Default TRUE.

Value

a ggplot of the barplot of assay data.

Examples

data("mouseBrainSubsetSCE")
plotSCEBarAssayData(
  inSCE = mouseBrainSubsetSCE,
  feature = "Apoe", groupBy = "sex"
)