plotMarkers: Plot Differential Markers
In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

plotMarkers

R Documentation

Plot Differential Markers

Description

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

Usage

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.