plotSCEBarAssayData {singleCellTK} | R Documentation |
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 = 1, transparency = 1, defaultTheme = TRUE, gridLine = FALSE, summary = NULL, title = NULL, titleSize = NULL, combinePlot = TRUE )
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 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. |
a ggplot of the barplot of assay data.
plotSCEBarAssayData( inSCE = mouseBrainSubsetSCE, feature = "Apoe", groupBy = "sex" )