In montilab/bieulergy: Interactive analysis of multi-omics regulatory networks

knitr::opts_chunk$set(comment="", cache=FALSE, fig.align="center", message=FALSE, warning=FALSE)
devtools::load_all(".")

Working with interactive network objects makes it easy to perform interactive analyses in Shiny and continue in the command line for extending analysis where you left off.

yeast.networks <- readRDS(file.path(system.file("extdata", package="bieulergy"), "yeast-networks.rds"))

Using Interactive Omics Network Objects

Network objects are essentially undirected igraph objects with pre-computed graph and node level properties. Additionally, they allow a mapping of unique node identifiers to human-readable symbols. These symbols are typically gene or protein symbols. This allows for integrating enrichment-based analysis or incorporating node-level information into network analyses.

network <- yeast.networks[[1]]

print(network)

Object Structure

str(network)

head(network$nodes)
head(network$edges)

Converting unique nodes identifiers to mapped symbols

network$get.symbols(c("749", "109", "740"))

Find interactors or filter sub networks

network$get.interactors(c("109"))
network$get.interactors(c("109", "107"))

network$plt.subnetwork(ids=c("109", "107"))
network$plt.subnetwork(ids=c("109", "107"), indirect.edges=TRUE)

network$plt.subnetwork(ids=c("109", "107"), degree=3)

network$plt.subnetwork(ids=c("109", "107"), degree=3, use.symbols=TRUE)

network$plt.subnetwork(ids=c("109", "107"), degree=3, use.symbols=TRUE, node.color="degree")

network$plt.subnetwork(ids=c("109", "107"), degree=5, use.symbols=TRUE, node.color="degree", layout="layout_on_grid")

network$plt.subnetwork(ids=c("109", "107", "607"), degree=0)

Omics Accessory Data

What if we have lots of multi-omics data we'd like to incorporate into the node/edge properties?

network$plt.subnetwork(ids=c("285"),
                       degree=2,
                       use.symbols=TRUE,
                       node.size="eigen",
                       node.color=list("lfc_mrna", cfx(c("blue", "white", "red"))),
                       node.border=list("snp_frq", cfx(c("#e9e9e9", "black"))),
                       node.shape="is_tf")

Sub Network Enrichment

What if we wanted to test enrichment of biological pathways within a sub network?

library(hypeR)
genesets <- enrichr_download(genesets="KEGG_2019", db="YeastEnrichr")

signature <- network$get.interactors(ids=c("285"), degree=2, remove.ids=FALSE, use.symbols=TRUE)
head(signature)

hyp <- hypeR(signature, genesets, background=16454)
hyp_dots(hyp)

head(hyp$data[,2:6])