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,
  rastr = TRUE
)

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").
rastr: A boolean value that indicates whether the plot should be rasterized using ggrastr. This does not rasterize lines and labels, just the internal portions of the plot.

Examples


#Get Test Project
proj <- getTestProject()

#Get Markers
seMarker <- getMarkerFeatures(
  ArchRProj = proj, 
  useMatrix = "PeakMatrix", 
  testMethod = "binomial", 
  binarize = TRUE
)

#Plot Markers
p <- plotMarkers(seMarker, name = "C1")

#PDF
plotPDF(p, name = "Marker-Plot", ArchRProj = proj)