Plot Differential Markers

This function will plot one group/column of a differential markers as an MA or Volcano plot.

plotMarkers(
  seMarker = NULL,
  name = NULL,
  cutOff = "FDR <= 0.01 & abs(Log2FC) >= 0.5",
  plotAs = "Volcano",
  scaleTo = 10^4
)

Arguments

seMarker

A SummarizedExperiment object returned by getMarkerFeatures().

name

The name of a column in seMarker (i.e. cell grouping in groupBy or useGroups for getMarkerFeatures()) to be plotted. To see available options try colnames(seMarker).

cutOff

A valid-syntax logical statement that defines which marker features from seMarker will be plotted. cutoff can contain any of the assayNames from seMarker.

plotAs

A string indicating whether to plot a volcano plot ("Volcano") or an MA plot ("MA").