01-data: GPML GraphingR Data

In WayFindR: Computing Graph Structures on WikiPathways

GPML GraphingR Data

Description

Our standard colors, line types (for edges), and shapes (for nodes) to display graph features from WikiPathways GPML files.

Usage

data(edgeColors)
data(edgeTypes)
data(nodeColors)
data(nodeShapes)

Format

There are four different objects.

edgeColors

A named character vector defining the colors used to display 17 different kinds of edges.

edgeTypes

A named character vector defining the line types (solid, dashed, etc.) used to display 17 different kinds of edges.

nodeColors

A named character vector defining the colors used to display 16 different kinds of nodes.

nodeShapes

A named character vector defining the symbols used to display 16 different kinds of nodes.

Author(s)

Kevin R. Coombes [e-mail], Polina Bombina [e-mail]

Source

We downloaded the complete set of 889 human (Homo sapiens) pathways from WikiPathways, in GPML format, at the end of March 2024. We wrote and ran perl scripts to iterate over this set of pathways and extract all the node types and all the edge types used anywhere in the set. We added a handful of node types (Undefined, Shape, Label, EDGE) in order to enable almost all of the pathways to be converted into mathematical graphs. We then defined colors and shapes to be used to distinguish different types in plots.

The situation with edges was slightly more complicated. The pathway editor (PathVisio; https://pathvisio.org/) typically used to create pathways in WikiPathways supports two different biologically meaningful vocabularies for edges: Molecular Interaction Maps (MIM; https://discover.nci.nih.gov/mim/formal_mim_spec.pdf) and System Biology Graphical Notation (SBGN; https://sbgn.github.io/), along with a very simple descrption as "Arrows" or "TBars". To make things more consistent, we converted both the SBGN and simple systems to match the MIM specification. We then defined colors and edge types so we could distinguish different edge types in plots.

Examples

data(edgeColors)
data(edgeTypes)
data(nodeColors)
data(nodeShapes)
if (require(Polychrome)) {
  swatch(edgeColors)
  swatch(nodeColors)
}
plot(0,0, type = "n", xlab="", ylab = "")
legend("center", legend = names(edgeColors),  lwd = 3,
       col = edgeColors,  lty = edgeTypes)
num <- c(rectangle = 15, circle = 16)
plot(0,0, type = "n", xlab="", ylab = "")
legend("center", legend = names(nodeColors),  cex = 1.5,
       col = nodeColors,  pch = num[nodeShapes])

WayFindR documentation built on June 30, 2024, 3 a.m.