RamiGO (version 1.18.0)

getAmigoTree: Getting the DAG GO tree for a set of GO ID's.

Description

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.

Usage

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)

Arguments

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.

Value

res

string with the webserver response.

Details

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.

Examples

## 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")