Plot Differential Markers — plotMarkers • ArchR

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").