PlotValues.PSI.Pseudobulk.Heatmap.10x: Heatmap of pseudo-bulk PSI values across different cell...

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

Heatmap of pseudo-bulk PSI values across different cell groups

Description

Heatmap of pseudo-bulk PSI values. x-axis represent main cell group, e.g. donor. y-axis represent sub-cell group, e.g. cell type

Usage

PlotValues.PSI.Pseudobulk.Heatmap.10x(
  MarvelObject,
  coord.intron,
  x.column,
  y.column,
  x.levels,
  y.levels,
  xlabels.size = 8,
  ylabels.size = 8,
  min.pct.cells.gene.expr = 10,
  min.n.cells.gene.expr = 10,
  min.gene.counts.total = 3
)

Arguments

MarvelObject	Marvel object. S3 object generated from CheckAlignment.10x function.
coord.intron	Character string. Coordinates of splice junction whose expression will be plotted.
x.column	Character string. Column name in MarvelObject$sample.metadata to indicate main-cell groups.
y.column	Character string. Column name in MarvelObject$sample.metadata to indicate sub-cell groups.
x.levels	Vector of character strings. Main cell groups to include for plotting.
y.levels	Vector of character strings. Sub-cell groups to include for plotting.
xlabels.size	Numeric value. Font size of heatmap column (main cell group) labels. Default is 8.
ylabels.size	Numeric value. Font size of heatmap row (sub-cell group) labels. Default is 8.
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.

Value

An object of class S3 with new slots MarvelObject$adhocPlot$Heatmap$Pseudobulk$Plot and MarvelObject$adhocPlot$Heatmap$Pseudobulk$Data.

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