在igraph中修复节点

Question

I have a directed graph where there is a start and an end node and they are defined such that no node leaves end and no node enters start. In my graph I want to fix the node start at the top of the graph and the end at the bottom with the intermediate nodes staying in between. How can I achieve this?

> final_data_graph
             (conversion) (start)      alpha       beta        delta     epsilon        eta       gamma       iota       kappa     lambda           mi      theta
(conversion)   0.00000000       0 0.00000000 0.00000000 0.000000e+00 0.000000000 0.00000000 0.000000000 0.00000000 0.000000000 0.00000000 0.000000e+00 0.00000000
(start)        0.00000000       0 0.03771482 0.14413063 8.571551e-05 0.006128659 0.18025972 0.013071615 0.47426392 0.002914327 0.03891484 4.285776e-05 0.10118716
alpha          0.18078800       0 0.58092440 0.03215991 1.049263e-04 0.017732543 0.03667174 0.002675620 0.06395257 0.005666020 0.03242222 0.000000e+00 0.03840302
beta           0.09504413       0 0.08766124 0.35022064 8.486083e-05 0.009164969 0.24753904 0.004327902 0.12075696 0.004752206 0.02274270 0.000000e+00 0.04760692
delta          0.53333333       0 0.00000000 0.00000000 0.000000e+00 0.066666667 0.00000000 0.000000000 0.26666667 0.066666667 0.00000000 0.000000e+00 0.06666667
epsilon        0.38628763       0 0.13991081 0.04347826 0.000000e+00 0.105351171 0.08193980 0.005574136 0.10200669 0.007246377 0.05128205 0.000000e+00 0.05351171
eta            0.42928641       0 0.11002583 0.09969325 0.000000e+00 0.023167582 0.19058767 0.002421698 0.07402325 0.008072328 0.01840491 0.000000e+00 0.03535680
gamma          0.28192371       0 0.14427861 0.05804312 0.000000e+00 0.021558872 0.08291874 0.066334992 0.15754561 0.018242123 0.05306799 0.000000e+00 0.09950249
iota           0.23902022       0 0.06370199 0.04091585 1.102111e-04 0.009202623 0.03240205 0.001790930 0.53868408 0.004573759 0.02669863 5.510553e-05 0.03160302
kappa          0.43064985       0 0.06886518 0.03685742 9.699321e-04 0.018428710 0.06498545 0.002909796 0.09602328 0.128031038 0.05431620 0.000000e+00 0.08244423
lambda         0.34914361       0 0.08695652 0.02561850 5.855658e-04 0.020348412 0.02547211 0.002488655 0.07539160 0.034401991 0.31620553 0.000000e+00 0.04977309
mi             0.00000000       0 0.25000000 0.00000000 0.000000e+00 0.000000000 0.00000000 0.000000000 0.50000000 0.000000000 0.00000000 2.500000e-01 0.00000000
theta          0.13940821       0 0.17562196 0.07949360 1.472104e-04 0.025320183 0.07198587 0.004269101 0.13513911 0.019431768 0.20491683 0.000000e+00 0.12939791
zeta           0.09929633       0 0.15871775 0.07427678 0.000000e+00 0.039874902 0.07974980 0.001563722 0.23612197 0.007036747 0.08444097 0.000000e+00 0.07271306
                    zeta
(conversion) 0.000000000
(start)      0.001285733
alpha        0.008499029
beta         0.010098439
delta        0.000000000
epsilon      0.023411371
eta          0.008960284
gamma        0.016583748
iota         0.011241528
kappa        0.015518914
lambda       0.013614405
mi           0.000000000
theta        0.014868247
zeta         0.146207975

ig <- graph.adjacency(final_data_graph, mode="directed", weighted=TRUE)

plot(ig,edge.label=round(E(ig)$weight,3),edge.width=.01,edge.arrow.size=.05,layout=layout.reingold.tilford(ig, root=which(V(ig)$name=='(start)')),vertex.color="white")

Answer 1

I assume you want to plot your graph with the start node at the top and end at the bottom. If so, you can use layout.reingold.tilford eg :

library(igraph)

# example graph
g <- graph.empty(directed = T)
g <- g + vertices(c('D','A','E','F','C','B'))
g <- g + edge('A','B')
g <- g + edge('A','C')
g <- g + edge('B','E')
g <- g + edge('B','D')
g <- g + edge('C','D')
g <- g + edge('D','F')
g <- g + edge('E','F')

# create the layout specifying the root node (i.e. start)
ly <- layout.reingold.tilford(g, root=which(V(g)$name=='A'),flip.y=T)
# let's plot
plot.igraph(g,layout=ly)