Plot Differential Expression Analysis Results (Deprecated)

plotDEA() has been renamed to plotPbDE() for clarity. This function is provided for backward compatibility and will be removed in a future version.

Usage

plotDEA(x, ...)

# S3 method for class 'TDRObj'
plotDEA(
  x,
  .dea.obj,
  .coefs = colnames(x = .dea.obj$coefficients),
  .order.by = "clustering",
  .markers = NULL,
  .q = 0.1,
  .row.space.scaler = 0.2,
  .col.space.scaler = 0.065,
  .label.substr.rm = "",
  ...
)

Arguments

x

A TDRObj, Seurat, SingleCellExperiment, or HDF5AnnData (anndataR) object.

.dea.obj

Differential expression results from get.dea() or get.pbDE().

.coefs

Character vector of coefficient names to plot.

.order.by

Character: "clustering" or "celltyping".

.markers

Character vector of feature names.

.q

Numeric adjusted p-value threshold.

.row.space.scaler

Numeric row height scaling.

.col.space.scaler

Numeric column width scaling.

.label.substr.rm

Character substring to remove from labels.

Value

A ggplot heatmap.

See also

plotPbDE