pathNetPlot.upstream: To present a net plot for pathways and upstream associated LR...

In yingyonghui/CommPath:

To present a net plot for pathways and upstream associated LR interactions

Description

To present a net plot for pathways and upstream associated LR interactions

Usage

pathNetPlot.upstream(
  object,
  select.ident,
  ident.col = NULL,
  vert.size.attr = "degree",
  vert.size.LR = 0.5,
  vert.size.path.adj = 5,
  top.n.path = NULL,
  path.order = "P.val.adj",
  select.path = "all",
  layout = "layout.auto",
  LR.label = "LR",
  pathway.label = TRUE,
  edge.arrow.size = 0.2,
  edge.color = "gray75",
  vertex.label.cex.LR = 0.5,
  vertex.label.cex.path = 0.5,
  vertex.label.color = "black",
  vertex.label.family = "Helvetica",
  vertex.frame.color = "#ffffff",
  node.pie = TRUE,
  return.net = FALSE,
  return.data = FALSE
)

Arguments

object	CommPath object
select.ident	Cluster of interest
ident.col	Vector of colors of each cluster; names of the col vector are supposed to be assigned to indicate each color for each cluster
vert.size.attr	Which statistical measures should be mapped to the size of vertex; Type "getNetAttr(object)" to retrieve the available statistical measures for pathways
vert.size.LR	Size of node representing LR interactions
vert.size.path.adj	pseudocount to adjust the size of node representing pathways
top.n.path	Top n activated pathways in the selected cluster of interest; if NULL, slelect all activated pathways
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; default is "P.val.adj". This parameter would be masked if top.n.path is set as NULL.
select.path	Vector of pathways for which users want to present a chain plot; default is all, which means to plot all pathways. The parameters top.n.path and path.order would be masked if this one is set with specific pathways.
layout	Network layout; defualt is Fruchterman-Reingold ('layout.fruchterman.reingold'). Refer to the igraph package for more information. Note: an error would be raised if the selected layout do not apply to the graph.
LR.label	To show which label on the node representing LR interactions. Available options: LR (to show both the ligand and receptor label), L (to show only the ligand label), R (to show only the receptor label), or NA (no label); default is NA
pathway.label	Logical value indicating to display the label of pathways or not; default is TRUE
edge.arrow.size	Size of arrow
edge.color	Color of edge
vertex.label.cex.LR	Font size of LR label
vertex.label.cex.path	Font size of pathway label
vertex.label.color	color of vertex label
vertex.label.family	Font family of the label
vertex.frame.color	Color of Node border
node.pie	Logical value indicating to show the node representing pathways in pie charts or not; default is TRUE
return.net	Logical value indicating to return the igraph object or not; default is FALSE
return.data	Logical value indicating to return the link dataframe or not; default is FALSE. This parameter allows users to export the link data in a dataframe, which could be analyzed in other network visualization tools, for example Cytoscape.

Value

Net plot showing the activated pathways and associated LR interactions

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