plot_topo {dSimer} | R Documentation |
plot topological relationship of two gene sets (which are associated with two diseases respectively).
plot_topo(geneset1, geneset2, graph, vertexcolor = c("tomato", "orange", "lightsteelblue"), vertex.shape = "circle", vertex.size = 14, vertex.label.font = 1, vertex.label.dist = 0, vertex.label.color = "black", vertex.label.cex = 0.5, edge.color = "black", layout = layout.auto)
geneset1 |
a character vector contains gene ids |
geneset2 |
another character vector contains gene ids |
graph |
an igraph graph object which represents a gene network |
vertexcolor |
a character vector contains 3 colors for vertexs |
vertex.shape |
vertex shape |
vertex.size |
vertex size |
vertex.label.font |
label text font |
vertex.label.dist |
label text dist |
vertex.label.color |
label text color |
vertex.label.cex |
label text cex |
edge.color |
edge color |
layout |
layout |
an igraph plot object
Peng Ni, Min Li
data("PPI_HPRD") g<-graph.data.frame(PPI_HPRD,directed = FALSE) #get an igraph graph data(d2g_fundo_symbol) a<-d2g_fundo_symbol[["DOID:8242"]] # get gene set a b<-d2g_fundo_symbol[["DOID:4914"]] # get gene set b plot_topo(a,b,g)