Going crazy with forceNetwork in R: no edges displayed

Question

I\'ve been trying to plot a network using networkD3 package in R for a week now. The simpleNetwork function works normally, but it doesn\'t allow much

Answer 1

Technically speaking, the reason your example data will not work, even if you address other possible problems (like edg$Gene1 and edg$Gene2 being non-numeric), is because you refer to a node 22 in your edg data, which in "0-based index" terms points to the 23rd row of your vert data frame, which does not exist.

As has been pointed out, this is probably because it is in 1-based indexing and should be converted, which could easily be done with

edg$Gene1 <- edg$Gene1 - 1
edg$Gene2 <- edg$Gene2 - 1

Alternatively, one might have intended to refer to another node which, for whatever reason did not make it into the vert data frame, in which case that node would need to be added to the vert data frame, which could easily be done with (for example)...

vert <- rbind(vert, c(23,1,1))

---

You could test whether or not you refer to a node in your edj data that doesn't exist in your vert data with something like...

all(unique(c(edg$Gene1, edg$Gene2)) %in% (1:nrow(vert) - 1))
# [1] FALSE

which should return TRUE. If not, something's wrong.

You could determine which nodes are referred to in your edg data that do not exist in your vert data with...

unique(c(edg$Gene1, edg$Gene2))[which(!unique(c(edg$Gene1, edg$Gene2)) %in% (1:nrow(vert) - 1))]
# [1] 22

---

fully reproducible example adjusting the indices in edg to be "0-based"

edg <- read.csv(header = TRUE, colClasses = 'character', text = '
Gene1,Gene2,Prob
1,22,3
2,22,6
3,22,6
4,22,9
5,22,3
6,22,4
7,22,8
8,22,4
9,22,6
10,22,8
11,22,6
12,22,10
13,22,6
14,22,3
15,22,6
16,22,6
17,22,0
18,22,4
19,22,6
20,22,4
')

vert <- read.csv(header = TRUE, colClasses = 'character', text = '
Symbol,Chr,Expr
1,21,9
2,17,10
3,17,0
4,20,0
5,6,9
6,5,11
7,12,0
8,1,20
9,17,11
10,17,7
11,17,11
12,10,0
13,17,0
14,7,7
15,17,6
16,17,0
17,2,5
18,5,10
19,17,10
20,17,9
21,12,4
22,3,2
')

# cast to numeric just to be sure
edg$Gene1 <- as.numeric(edg$Gene1)
edg$Gene2 <- as.numeric(edg$Gene2)

# adjust the indices so they're "0-based"
edg$Gene1 <- edg$Gene1 - 1
edg$Gene2 <- edg$Gene2 - 1

# Nodesize is also necessarily numeric
vert$Expr <- as.numeric(vert$Expr)

library(networkD3)
forceNetwork(Links = edg, Nodes = vert, Source = "Gene1", Target = "Gene2", 
         Value = "Prob", NodeID = "Symbol", Group = "Chr", opacity = 0.7,
         Nodesize = "Expr", zoom = TRUE, legend = TRUE)

---

fully reproducible example adding a node to vert

edg <- read.csv(header = TRUE, colClasses = 'character', text = '
Gene1,Gene2,Prob
1,22,3
2,22,6
3,22,6
4,22,9
5,22,3
6,22,4
7,22,8
8,22,4
9,22,6
10,22,8
11,22,6
12,22,10
13,22,6
14,22,3
15,22,6
16,22,6
17,22,0
18,22,4
19,22,6
20,22,4
')

vert <- read.csv(header = TRUE, colClasses = 'character', text = '
Symbol,Chr,Expr
1,21,9
2,17,10
3,17,0
4,20,0
5,6,9
6,5,11
7,12,0
8,1,20
9,17,11
10,17,7
11,17,11
12,10,0
13,17,0
14,7,7
15,17,6
16,17,0
17,2,5
18,5,10
19,17,10
20,17,9
21,12,4
22,3,2
')

# cast to numeric just to be sure
edg$Gene1 <- as.numeric(edg$Gene1)
edg$Gene2 <- as.numeric(edg$Gene2)
vert$Expr <- as.numeric(vert$Expr)

# add another node to the Nodes data frame
vert <- rbind(vert, c(23,1,1))

library(networkD3)
forceNetwork(Links = edg, Nodes = vert, Source = "Gene1", Target = "Gene2", 
         Value = "Prob", NodeID = "Symbol", Group = "Chr", opacity = 0.7,
         Nodesize = "Expr", zoom = TRUE, legend = TRUE)