getAmigoTree: Getting the DAG GO tree for a set of GO ID's.
In RamiGO: AmiGO visualize R interface

Description Usage Arguments Details Value Author(s) Examples

Getting the DAG GO tree for a set of GO ID's from AmiGO. Saves it as a png, svg or dot file. Returns the webserver response as a string.

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getAmigoTree(goIDs, color, pvalues, pcolors = c("white","tomato"),
  psplit = c(1,0.25,0.1,0.05,0.001), filename, picType = "png",
  modeType = "amigo", webserver, saveResult = TRUE)

`goIDs`	is a vector of GO ID's.
`color`	is a vector of colors(). Either of length 1 or length(goIDs).
`pvalues`	is a vector of pvalues.
`pcolors`	colors for gradient.
`psplit`	is a vector of pvalues that sets different color gradients ranges.
`filename`	is the output filename. If the file ending is missing or not matching the picType, the file ending is automatically fixed (replaced or created).
`picType`	supports "png","svg" and "dot". default is "png".
`modeType`	is the AmiGO query mode, only "amigo" is supported for AmiGO v2. If you're using AmiGO v1 use modeType="advanced".
`webserver`	is by default the AmiGO v2 webserver. You can specify another one.
`saveResult`	saving the result as a png, svg or dot file. Default is TRUE.

The edge colors in the tree represent the relationship between two nodes. In particular: green=positively regulates, red=negatively regulates, black=regulates, blue=is a, light blue=part of. The tree represents the set of input GO ID's and all parents of those GO ID's.

res

string with the webserver response.

Markus Schroeder <mschroed@jimmy.harvard.edu>

## set GO ID's and color
goIDs <- c("GO:0051130","GO:0019912","GO:0005783")
color <- c("lightblue","red","yellow")

## get results
pp <- getAmigoTree(goIDs=goIDs,color=color,filename="example")
ss <- getAmigoTree(goIDs=goIDs,color=color,filename="example",picType="svg",saveResult=FALSE)
dd <- getAmigoTree(goIDs=goIDs,color=color,filename="example",picType="dot",saveResult=FALSE)

#ppNoColor <- getAmigoTree(goIDs=goIDs,filename="example-no-color",saveResult=FALSE)

#goIDs <- c("GO:0051130","GO:0050789","GO:0019912","GO:0016301","GO:0003824","GO:0005783","GO:0043229")
#pvalues <- c(0.001,0.5,0.0001,0.16,0.47,0.00006,0.002)
#ptest <- getAmigoTree(goIDs=goIDs, pvalues=pvalues, filename="pvaluetest")