Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
## ----packs--------------------------------------------------------------------
library(WayFindR)
suppressMessages( library(igraph) )
## ----graph--------------------------------------------------------------------
xmlfile <- system.file("pathways/WP3850.gpml", package = "WayFindR")
G <- GPMLtoIgraph(xmlfile)
class(G)
## ----calcmetrics--------------------------------------------------------------
# Calculate metrics
metrics <- data.frame(nVertices = length(V(G)),
nEdges = length(E(G)),
nNegative = sum(edge_attr(G, "MIM") == "mim-inhibition"),
hasLoop = any_loop(G),
hasMultiple = any_multiple(G),
hasEuler = has_eulerian_cycle(G) | has_eulerian_path(G),
nComponents = count_components(G),
density = edge_density(G),
diameter = diameter(G),
radius = radius(G),
girth = ifelse(is.null(girth(G)), NA, girth(G)$girth),
nTriangles = sum(count_triangles(G)),
efficiency = global_efficiency(G),
meanDistance = mean_distance(G),
cliques = clique_num(G),
reciprocity = reciprocity(G))
metrics
## ----cyclesub-----------------------------------------------------------------
cy <- findCycles(G)
length(cy)
S <- cycleSubgraph(G, cy)
cymetrics <- data.frame(nCycles = length(cy),
nCyVert = length(V(S)),
nCyEdge = length(E(S)),
nCyNeg = sum(edge_attr(S, "MIM") == "mim-inhibition"))
cymetrics
## ----fig.width=8, fig.height=8, fig.cap = "Figure 1: Example pathway (WP3850) from WikiPathways."----
set.seed(93217)
plot(S)
nodeLegend("topleft", S)
edgeLegend("bottomright", S)
## ----degree-------------------------------------------------------------------
deg <- degree(G)
summary(deg)
tail(sort(deg))
## ----maxdeg-------------------------------------------------------------------
w <- which(deg == 12)
V(G)[w]$label
## ----splore-------------------------------------------------------------------
A <- adjacent_vertices(G, w, "in")
A
## ----in-genes-----------------------------------------------------------------
ids <- as_ids(A[[1]])
V(G)$label[as_ids(V(G)) %in% ids]
## ----edgeTypes----------------------------------------------------------------
Earg <- as.vector(t(as.matrix(data.frame(Source = ids, Target = names(w)))))
E(G, P = Earg)$MIM
## ----fig.width=7, fig.height=7, fig.cap="Figure 2: Immediate portion of the pathway aronud the mTORC1 complex."----
B <- adjacent_vertices(G, w, "out")
subg <- subgraph(G, c(names(w), ids, as_ids(B[[1]])))
plot(subg, lwd=3)
## ----seven--------------------------------------------------------------------
w <- which(deg == 7)
V(G)[w]$label
## ----fig.width=7, fig.height=7, fig.cap="Figure 3: Immediate portion of the pathway around `FoxO."----
B <- adjacent_vertices(G, w, "all")
subg <- subgraph(G, c(names(w), as_ids(B[[1]])))
plot(subg, lwd=3)
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