Question: Empty annotation of DOT objects with readAmigoDot() (no annot or leaves)
0
gravatar for evepash
4.0 years ago by
evepash0
evepash0 wrote:

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: 

 

ADD COMMENTlink written 4.0 years ago by evepash0

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: 

ADD REPLYlink written 3.1 years ago by pim20010
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