plot_path2gene: River plot of significantly activated pathways and related...

In ZJUFanLab/SpaTalk: Infer Cell-Cell Communication for Spatial Transcriptomics

River plot of significantly activated pathways and related downstream genes of receptors.

Description

River plot of significantly activated pathways and related downstream genes of receptors.

Usage

plot_path2gene(
  object,
  celltype_sender,
  celltype_receiver,
  ligand,
  receptor,
  min_gene_num = 5,
  pvalue = 0.5,
  color = NULL,
  color_flow = "blue"
)

Arguments

object	SpaTalk object generated from dec_cci.
celltype_sender	Name of celltype_sender.
celltype_receiver	Name of celltype_receiver.
ligand	Name of ligand from celltype_sender.
receptor	Name of receptor from celltype_receiver.
min_gene_num	Min genes number for each pathway.
pvalue	P value of the Fisher-exact test.
color	Color of pathways and genes. Two values.
color_flow	Color of the flow.

ZJUFanLab/SpaTalk documentation built on Jan. 21, 2025, 3:13 p.m.