PseudotimePlot: Plot dynamic changes along pseudotime trajectory

In CostaLab/scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference

Plot dynamic changes along pseudotime trajectory

Description

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

Usage

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

CostaLab/scMEGA documentation built on Sept. 25, 2024, 6:11 a.m.