Question: Vertices name in steinertree [R]
0
gravatar for anu014
2.2 years ago by
anu014180
India
anu014180 wrote:

Hello all,

Can anyone tell me how to retain the name of vertices in steinertree package (R)? Below is the code I used. The final object SP (igraph object) is the one that is showing node names as 1,2,3..

    library(igraph)
    library(SteinerNet)

    a <- read.table("interactions.txt", sep="\t", quote="")
    head(a)
                   V1
    1 ENSP00000222390
    2 ENSP00000391826
    3 ENSP00000222390
    4 ENSP00000391669
    5 ENSP00000222390
    6 ENSP00000384675

    el <- matrix(as.vector(a$V1), nc=2, byrow=T) 

    g1 =graph_from_edgelist(el, directed=F)

    ter_list= c("ENSP00000306512","ENSP00000340019","ENSP00000361125","ENSP00000367207","ENSP00000384273","ENSP00000388107","ENSP00000400175","ENSP00000401303")
    SP=steinertree(type ="SP",terminals = ter_list, graph = g1)

SP
[[1]]
IGRAPH 6a21ce1 UN-- 139 1600 -- 
+ attr: name (v/c), realname (v/c), color (v/c)
+ edges from 6a21ce1 (vertex names):
 [1] 1 --2  1 --3  1 --4  1 --5  1 --6  1 --7  1 --8  1 --9  1 --10 1 --11
[11] 1 --12 1 --13 1 --14 1 --15 1 --16 1 --17 1 --18 1 --19 1 --20 1 --21
[21] 1 --22 1 --23 1 --24 1 --25 1 --26 1 --27 1 --28 1 --29 1 --30 1 --31
[31] 1 --32 1 --33 34--35 34--36 34--37 34--38 9 --34 34--39 20--34 34--40
[41] 25--34 27--34 34--41 34--42 34--43 34--44 35--45 45--46 45--47 45--48
[51] 38--45 45--49 39--45 40--45 45--50 30--51 3 --30 4 --30 30--52 30--53
[61] 30--54 5 --30 30--48 30--55 8 --30 30--56 9 --30 10--30 30--57 11--30
[71] 15--30 30--58 20--30 21--30 30--59 25--30 30--60 27--30 28--30 3 --61
+ ... omitted several edges

[[2]]
IGRAPH 886b59f UN-- 12 11 -- 
+ attr: name (v/c), realname (v/c), color (v/c)
+ edges from 886b59f (vertex names):
 [1] 5 --8  5 --19 5 --21 5 --50 35--50 5 --51 21--53 5 --61 8 --69 53--73
[11] 5 --84

Please help me out. Thank you for the effort :)

graph ppi gene • 620 views
ADD COMMENTlink written 2.2 years ago by anu014180
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2033 users visited in the last hour