pathChainPlot: To present the interactions for a selected cluster, including...

In yingyonghui/CommPath:

To present the interactions for a selected cluster, including both the upstream and downstream clusters which are connected by specific pathways in the selected cluster

Description

To present the interactions for a selected cluster, including both the upstream and downstream clusters which are connected by specific pathways in the selected cluster

Usage

pathChainPlot(
  object,
  select.ident,
  up.ident = NULL,
  down.ident = NULL,
  acti.path.dat = NULL,
  top.n.path = 5,
  path.order = "P.val.adj",
  select.path = "all",
  p.thre = 0.05,
  top.n.receptor = 10,
  top.n.ligand = 10,
  dot.ident.col = NULL,
  dot.ident.size = 1,
  dot.gene.col = NULL,
  dot.gene.size = 1,
  bar.pathway.col = NULL,
  label.text.size = 1,
  label.title.size = 1
)

Arguments

object	CommPath object
select.ident	Plot the activated pathways for which cluster or cell type?
up.ident	Upstream clusters in the communication chain; default is all clusters
down.ident	down.ident clusters in the communication chain; default is all clusters
acti.path.dat	Data frame of differential activation test result from diffAllPath
top.n.path	Top n pathways with the smallest adjusted p values to plot
path.order	Sort criteria used to select the top n pathways, either 'P.val' or 'P.val.adj', which represent the original and adjusted p values, or 'diff' which represents the mean (in t test) or median (in wilcox test) difference
select.path	Vector of pathways for which users want to present a chain plot; default is all, which means to plot all pathways. The parameter top.n.path would be masked if this one is set with specific pathways.
p.thre	Threshold for adjust p values; Only pathways with a adjust p valua < p.thre would be considered
top.n.receptor	Top n receptor with the largest log2FCs to plot
top.n.ligand	Top n ligand with the largest log2FCs to plot
dot.ident.col	Color of the dots representing clusters
dot.ident.size	Size of the dots representing clusters
dot.gene.col	Color of the dots representing receptors and ligands
dot.gene.size	Size of the dots representing receptors and ligands
bar.pathway.col	Color of the bars reprsenting pathways
label.text.size	Text size in the plot
label.title.size	Text size of the title annotation of the plot

Value

Network plot showing receptors in the selected cluster, the upstream clusters which show L-R connections with the selected cluster, and the significant pathways involved in the receptors

yingyonghui/CommPath documentation built on June 15, 2025, 6:29 a.m.