zoomPathway: Zoom in on pathway in igraph

In drjingma/netgsa: Network-Based Gene Set Analysis

Description

Plots the gene to gene interactions for a given pathway in igraph.

Usage

zoomPathway(x, pway, graph_layout = NULL)

Arguments

x	A NetGSA object returned from calling NetGSA()
pway	Name of pathway to plot
graph_layout	(Optional) Layout function to pass to igraph plots. This function should only take one parameter (an igraph object). For example one might create a custom layout by setting the spring.length and spring.constant with: my_layout <- function(graph) layout_with_graphopt(graph = graph, spring.length = 1000, spring.constant = 0.00004)

Details

Generates igraph plot for gene to gene interactions for a given pathway

Value

No return value, called to zoom to pathway

Author(s)

Michael Hellstern

References

Ma, J., Shojaie, A. & Michailidis, G. (2016) Network-based pathway enrichment analysis with incomplete network information. Bioinformatics 32(20):165–3174.

See Also

plot.NetGSA

Examples

library(igraph)

## load the data
data("breastcancer2012")

## consider genes from the "ErbB signaling pathway" and "Jak-STAT signaling pathway"
genenames    <- unique(c(pathways[[24]], pathways[[52]]))
sx           <- x[match(rownames(x), genenames, nomatch = 0L) > 0L,]

db_edges       <- obtainEdgeList(rownames(sx), databases = c("kegg", "reactome", "biocarta"))
adj_cluster    <- prepareAdjMat(sx, group, databases = db_edges, cluster = TRUE)
out_cluster    <- NetGSA(adj_cluster[["Adj"]], sx, group, pathways_mat[c(24, 52), rownames(sx)], lklMethod = "REHE", sampling = FALSE, sample_n = 0.1, sample_p = 0.1)

### Cytoscape closed or open
plot(out_cluster) 
my_layout <- function(graph) layout_with_graphopt(graph = graph, spring.length = 1000, spring.constant = 0.00004)
zoomPathway(out_cluster, "ErbB signaling pathway", my_layout)

drjingma/netgsa documentation built on Feb. 22, 2022, 5:18 p.m.