删除没有边的自循环和顶点

Question

我正在构建一个基因网络.我有一个两列数据框,我转换成和邻接矩阵,并在igraph中使用它.问题是我有自我循环的基因,我想摆脱自我循环,然后摆脱没有边缘(可能与网络隔离)的顶点.我尝试了一些东西,但不知怎的,它们不起作用.我的代码是

 InnatedGraph <- graph.data.frame(innate,directed=FALSE)
 V(InnatedGraph)$label.cex = 0.4
 plot(InnatedGraph,vertex.label=V(InnatedGraph)$symbol, vertex.size=5)

先天是我的两列数据框架.我已经尝试过度函数去除0度的顶点,但我猜不幸它不起作用(也许becoz自环基因有1度).

bad.vs<-V(InnatedGraph)[degree(InnatedGraph) == 0] 
clean <-delete.vertices(InnatedGraph, bad.vs)

我尝试使用包装BioNet"rmSelfLoops"中的另一个函数,借助它我可以移除自循环边但仍然无法移除没有边的顶点.

test<-rmSelfLoops(InnatedGraph)

我还将包含我的网络图片,以便更容易理解.

Answer 1

考虑这个示例图及其两个子集/修改:

library(igraph)
set.seed(1)
g <- random.graph.game(10, p.or.m = 3, "gnm") + edge(7,7)
coords <- layout.auto(g)
par(mfrow = c(1,3))
plot(g, layout = coords)
plot(simplify(g), layout = coords) # remove loops and multiple edges
plot(delete.vertices(simplify(g), degree(g)==0)) # additionally delete isolated nodes

使用评论中的OP样本数据:

df <- read.csv(header=F, row.names = 1, stringsAsFactors=F, text='"53","ENSG00000175104","ENSG00000175104"
"54","ENSG00000174775","ENSG00000175104"
"55","ENSG00000032688","ENSG00000027164"
"56","ENSG00000175104","ENSG00000140968"
"57","ENSG00000027164","ENSG00000041515"
"58","ENSG00000027164","ENSG00000025498"')
library(igraph)
( dfclean <- subset(df, V2!=V3) ) # remove rows where source==target
#                V2              V3
# 54 ENSG00000174775 ENSG00000175104
# 55 ENSG00000032688 ENSG00000027164
# 56 ENSG00000175104 ENSG00000140968
# 57 ENSG00000027164 ENSG00000041515
# 58 ENSG00000027164 ENSG00000025498
par(mfrow = c(1,3))
plot(graph_from_data_frame(df), edge.arrow.size = .5) # orig
plot(simplify(graph_from_data_frame(df)), edge.arrow.size = .5) # same as
plot(graph_from_data_frame(dfclean), edge.arrow.size = .5) # this one