Description Usage Arguments Value Author(s) Examples
Create R graphical objects of an iRefIndex/edgeList interaction table.
1 2 | convert_edgeList_to_graph(edgeList, directionality, graphical_package)
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edgeList |
iRefIndex/edgeList R table. |
directionality |
Either "directed" for directed graphs or "undirected" for undirected graphs. The chosen value must be the same used to generate the edgeList table. Default="undirected". |
graphical_package |
Either "graph" or "igraph", depending on the R package the user wants to use. If you use "graph", no loop edges will be allowed. Default="igraph". |
output |
R graphical object corresponding to the original edgeList. |
Antonio Mora <antoniocmora@gmail.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 | ## get tables
irefindex_curr_ecoli = get_irefindex("562", "13.0", tempdir())
all_INTACT = select_database("intact", irefindex_curr_ecoli)
binary_INTACT = select_interaction_type("binary", all_INTACT)
complex_INTACT = select_interaction_type("complex", all_INTACT)
edgeList_binary_INTACT = convert_MITAB_to_edgeList(binary_INTACT)
edgeList_complex_INTACT_s = convert_MITAB_to_edgeList(complex_INTACT, "default",
"spoke")
edgeList_complex_INTACT_m = convert_MITAB_to_edgeList(complex_INTACT, "default",
"matrix")
edgeList_all_INTACT = convert_MITAB_to_edgeList(all_INTACT, "default", "spoke")
edgeList_binary_INTACT_dir = convert_MITAB_to_edgeList(binary_INTACT, "default",
"bipartite", "yes", "directed")
edgeList_complex_INTACT_sdir = convert_MITAB_to_edgeList(complex_INTACT, "default",
"spoke", "yes", "directed")
## execute function
graph_binary_INTACT = convert_edgeList_to_graph(edgeList_binary_INTACT,
"undirected", "igraph")
graph_complex_INTACT_s = convert_edgeList_to_graph(edgeList_complex_INTACT_s)
graph_complex_INTACT_m = convert_edgeList_to_graph(edgeList_complex_INTACT_m)
## Not run:
graph_all_INTACT = convert_edgeList_to_graph(edgeList_all_INTACT)
graph_binary_INTACT_dir = convert_edgeList_to_graph(edgeList_binary_INTACT_dir,
"directed")
graph_complex_INTACT_sdir = convert_edgeList_to_graph(edgeList_complex_INTACT_sdir,
"directed")
# For the binary case, edge number is smaller than the undirected case because only
# interactions with bait information are used. For the complex spoke case, the edge
# number is bigger than the undirected case because edges with two baits give raise
# to two directed edges and only one undirected.
## Additional info if you are using "graph":
library(Rgraphviz)
edgeList_complex = convert_MITAB_to_edgeList(complex_INTACT, node_names="uids")
graph_complex = convert_edgeList_to_graph(edgeList_complex, graphical_package=
"graph")
plot(graph_complex, "neato")
nodes(graph_complex)
edges(graph_complex)
degree(graph_complex)
numNoEdges(graph_complex)
mostEdges(graph_complex)
adj(graph_complex,"uniprotkb:P28043")
acc(graph_complex, "uniprotkb:P28043")
sg <- subGraph(nodes(graph_complex)[1:20], graph_complex)
plot(sg, "neato")
## Additional info if you are using "igraph":
V(graph_binary_INTACT)$name
V(graph_binary_INTACT)[igraph::degree(graph_binary_INTACT) == 1]$name
par(mfrow=c(2,3))
plot(graph_binary_INTACT, layout=layout.fruchterman.reingold, vertex.size=3,
vertex.color="green", frame=TRUE, main="Binary", vertex.label=NA)
plot(graph_complex_INTACT_s, layout=layout.fruchterman.reingold, vertex.size=3,
vertex.color="green", frame=TRUE, main="Complex Spoke", vertex.label=NA)
plot(graph_complex_INTACT_m, layout=layout.fruchterman.reingold, vertex.size=3,
vertex.color="green", frame=TRUE, main="Complex Matrix", vertex.label=NA)
plot(graph_all_INTACT, layout=layout.fruchterman.reingold, vertex.size=3,
vertex.color="green", frame=TRUE, main="Binary and Complex Spoke", vertex.label=NA)
plot(graph_binary_INTACT_dir, layout=layout.fruchterman.reingold, vertex.size=3,
edge.arrow.size=0.3, vertex.color="green", frame=TRUE, main="Binary Directed",
vertex.label=NA)
plot(graph_complex_INTACT_sdir, layout=layout.fruchterman.reingold, vertex.size=3,
edge.arrow.size=0.3, vertex.color="green", frame=TRUE, main="Complex Spoke Directed",
vertex.label=NA)
x11(); par(mfrow=c(1,2))
plot(degree.distribution(graph_binary_INTACT), main="Degree Distribution (Binary,
INTACT, E.coli)")
plot(degree.distribution(graph_binary_INTACT),log="xy", main="Log-Log Degree
Distribution (Binary, INTACT, E.coli)")
## End(Not run)
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