In montilab/hypeR-next: Network Enrichment

knitr::opts_chunk$set(message=FALSE, warning=FALSE, comment="")
devtools::load_all(".")
library(igraph)
library(hypeR)

hypeR Network Extension

An extension of hypeR for network enrichment through random walks.

Installation

devtools::install_github("montilab/hypeR-next")

library(hypeR.next)

Data

data(ig)

This package works with undirected igraph objects or extensions of igraph objects.

is(ig)

The following vertex attributes are expected at a minimum.

name - Unique node labels
symbol - Node symbols corresponding to the genesets you use
community- Pre-detected community labels
color - Community-specific colors

head(igraph::as_data_frame(ig, what="vertices"))

set.seed(1)
layout <- igraph::layout_with_graphopt(ig, 
                                       start=NULL, 
                                       niter=1000,
                                       charge=0.005,
                                       mass=30, 
                                       spring.length=0,
                                       spring.constant=1, 
                                       max.sa.movement=5)

par(mar=c(0,0,0,0))
plot(ig,
     vertex.size=4,
     vertex.color="grey",
     vertex.frame.color="black",
     vertex.label=NA,
     edge.width=1,
     layout=layout)

Network characterization through random walks

library(hypeR)
genesets <- hypeR::msigdb_gsets("Homo sapiens", "H", clean=TRUE)

ig.e <- enrich_communities_static(ig, genesets, restart=0.5, fdr=0.01, top=1)

par(mar=c(0,0,0,0))
set.seed(1234)
plot(ig.e,
     vertex.size=5,
     vertex.label=V(ig.e)$enrichment,
     vertex.color=adjustcolor(V(ig.e)$color, alpha.f=0.6),
     vertex.frame.color=adjustcolor("#000000", alpha.f=0),
     vertex.label.family="Helvetica",
     vertex.label.color="black",
     vertex.label.font=2,
     vertex.label.cex=0.8,
     vertex.label.dist=runif(vcount(ig.e), -0.25, 0.25),
     edge.color=adjustcolor("#000000", alpha.f=0.2),
     layout=layout)