From a character vector of GO IDs (named GOhiIDs containing 142 GO IDs) and I used getAmigoTree and readAmigoDot to get a dot object:
getAmigoTree(GOhiIDs,filename="RamiGO", picType="dot", saveResult=TRUE)
Then I perform:
tt1 <- readAmigoDot(filename="RamiGO.dot")
If you look at tt1 all annotations for GO_ID are "NULL" (i.e. under tt1@leaves$GO_ID everything is null, even though leaves is a data.frame of 807 obs. of 6 variables). See below for details. Why are the annotations not there in tt1?
Thanks,
Evi
R version 3.2.0 (2015-04-16)
RamiGO_1.14.0
class: AmigoDot
Class 'igraph.es' atomic [1:1] 1
..- attr(*, "env")=<environment: 0x111cdebf0>
nodes:
Class 'igraph.vs' atomic [1:807] 1 2 3 4 5 6 7 8 9 10 ...
..- attr(*, "env")=<environment: 0x111c90898>
edges:
'data.frame': 0 obs. of 6 variables:
$ node : chr
$ GO_ID : chr
$ description: chr
$ color : chr
$ fillcolor : chr
$ fontcolor : chr
leaves:
'data.frame': 807 obs. of 6 variables:
$ node : chr "NULL" "NULL" "NULL" "NULL" ...
$ GO_ID : chr "NULL" "NULL" "NULL" "NULL" ...
$ description: chr "NULL" "NULL" "NULL" "NULL" ...
$ color : chr "NULL" "NULL" "NULL" "NULL" ...
$ fillcolor : chr "NULL" "NULL" "NULL" "NULL" ...
$ fontcolor : chr "NULL" "NULL" "NULL" "NULL" ...
annot:
'data.frame': 2153 obs. of 6 variables:
$ parent : chr "NULL" "NULL" "NULL" "NULL" ...
$ child : chr "NULL" "NULL" "NULL" "NULL" ...
$ arrowhead: chr "NULL" "NULL" "NULL" "NULL" ...
$ arrowtail: chr "NULL" "NULL" "NULL" "NULL" ...
$ color : chr "NULL" "NULL" "NULL" "NULL" ...
$ style : chr "NULL" "NULL" "NULL" "NULL" ...
relations:
Hi! I'm having the exact same problem. the getAmigoTree() seems to be working but the readAmigoDot() doesn't seem to be working. Were you able to find a solution or alternative?
Here's my code:
dotRes.BP <- getAmigoTree(goIDs=BP.goIDs, color=color.BP, filename="BP-go-tree", picType="dot", saveResult=TRUE)
tt.bp <- readAmigoDot(object=dotRes.BP) #this doesn't seem to be working
show(tt.bp)
class: AmigoDot
Class 'igraph.es' atomic [1:1] 1
..- attr(*, "vnames")= chr "NULL|NULL"
..- attr(*, "env")=<weakref>
..- attr(*, "graph")= chr "205d911f-e81e-437f-a11d-147f04f0d518"
nodes:
Class 'igraph.vs' atomic [1:93] 1 2 3 4 5 6 7 8 9 10 ...
..- attr(*, "env")=<weakref>
..- attr(*, "graph")= chr "205d911f-e81e-437f-a11d-147f04f0d518"
edges:
'data.frame': 0 obs. of 6 variables:
$ node : chr
$ GO_ID : chr
$ description: chr
$ color : chr
$ fillcolor : chr
$ fontcolor : chr
leaves:
'data.frame': 93 obs. of 6 variables:
$ node : chr "NULL" "NULL" "NULL" "NULL" ...
$ GO_ID : chr "NULL" "NULL" "NULL" "NULL" ...
$ description: chr "NULL" "NULL" "NULL" "NULL" ...
$ color : chr "NULL" "NULL" "NULL" "NULL" ...
$ fillcolor : chr "NULL" "NULL" "NULL" "NULL" ...
$ fontcolor : chr "NULL" "NULL" "NULL" "NULL" ...
annot:
'data.frame': 245 obs. of 6 variables:
$ parent : chr "NULL" "NULL" "NULL" "NULL" ...
$ child : chr "NULL" "NULL" "NULL" "NULL" ...
$ arrowhead: chr "NULL" "NULL" "NULL" "NULL" ...
$ arrowtail: chr "NULL" "NULL" "NULL" "NULL" ...
$ color : chr "NULL" "NULL" "NULL" "NULL" ...
$ style : chr "NULL" "NULL" "NULL" "NULL" ...
relations: