PlotValues.PSI.Pseudobulk.10x: Boxplot of pseudo-bulk PSI values vs cell groups

In wenweixiong/MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Boxplot of pseudo-bulk PSI values vs cell groups

Description

Boxplot of pseudo-bulk PSI values on the y-axis against cell groups on the x-axis.

Usage

PlotValues.PSI.Pseudobulk.10x(
  MarvelObject,
  cell.group.list,
  coord.intron,
  cell.group.colors = NULL,
  xlabels.size = 10,
  min.pct.cells.gene.expr = 10,
  min.n.cells.gene.expr = 3,
  min.gene.counts.total = 3,
  method = "t.test",
  p.adjust.method = "fdr"
)

Arguments

MarvelObject	Marvel object. S3 object generated from CheckAlignment.10x function.
cell.group.list	List of character strings. Each element in the list (main list) is a list (sub-list). Each sub-list in turn is a list of pseudobulk samples represented by cell IDs. Each element in the main list is a cell group and the label of each element of the main list represents the cell group label.
coord.intron	Character string. Coordinates of splice junction whose expression will be plotted.
cell.group.colors	Vector of character strings. Colors of cell groups and should be same length as cell.group.list. Default ggplot2 colors are used.
xlabels.size	Numeric value. Font size of x-tick labels. Default is 10.
min.pct.cells.gene.expr	Numeric value. Percentage of cell expressing the gene in a pseudobulk, below which, the pseudobulk will be omitted from plotting. Default is 10.
min.n.cells.gene.expr	Numeric value. Number of cell expressing the gene in a pseudobulk, below which, the pseudobulk will be omitted from plotting. Default is 3.
min.gene.counts.total	Numeric value. Totol gene counts in a pseudobulk, below which, the pseudobulk will be omitted from plotting. Default is 3.
method	Character string. Statistical test for all possible pair-wise comparisons. Options are "t.test" (default) or "wilcox".
p.adjust.method	Character string. Method for multiple testing adjustment as per method option of p.adjust function. Default is "fdr".

Value

An object of class S3 with new slots MarvelObject$adhocPlot$Boxplot$Pseudobulk$PSI$Plot, MarvelObject$adhocPlot$Boxplot$Pseudobulk$PSI$Stats, and MarvelObject$adhocPlot$Boxplot$Pseudobulk$PSI$Data.

wenweixiong/MARVEL documentation built on Aug. 5, 2024, 2:54 p.m.