Plot dynamic changes along pseudotime trajectory

This function will generate a line plot to visualize the TF binding activity, TF expression, and TF target expression along the trajectory.

PseudotimePlot(
  object,
  tf.use,
  tf.assay = "chromvar",
  rna.assay = "RNA",
  atac.assay = "ATAC",
  target.assay = "target",
  trajectory.name = "Trajectory",
  groupEvery = 1
)

Arguments

object

A Seurat object used as input.

tf.use

Which TF to plot.

tf.assay

Assay name for TF binding activity. Default: "chromvar"

rna.assay

Assay name for TF expression. Default: "RNA"

atac.assay

Assay name for Peaks. Default: "ATAC"

target.assay

Assay name for TF target expression. Default: "target"

trajectory.name

Trajectory name for visualization.

groupEvery

The number of sequential percentiles to group together when generating a trajectory. This is similar to smoothing via a non-overlapping sliding window across pseudo-time.

Value

A ggplot object