GRNSpatialPlot: Plot the target gene in spatial space

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

Plot the target gene in spatial space

Description

This function plots the overall expression of all target genes for a particular TF using spatial transcriptome data. It is based on

Usage

GRNSpatialPlot(
  object,
  assay,
  df.grn,
  tf.use,
  min.cutoff = "q5",
  max.cutoff = "q95",
  vis.option = "B",
  crop = TRUE
)

Arguments

object	A Seurat object of spatial transcriptome data
assay	Which assay to plot
df.grn	A data frame including the inferred gene regulatory network
tf.use	Which TF to use
min.cutoff	Minimum cutoff values for each feature
max.cutoff	Maximum cutoff values for each feature
vis.option	Options for visualization. Default: "B"

Value

A ggplot object

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