plotGOgraph: Function to draw and save gene ontology DAG.
In CLippmann/ORA: Overrepresentation Analysis

Description Usage Arguments Value Author(s) See Also

Function draws and colors the gene ontology DAG of input GO terms depending on input parameters and saves it as PlotFile.

plotGOgraph(Adj,GOtermIDs,PlotFile,PlotDirectory=getwd(),
	Significant=rep(1,length(GOtermIDs)),IsHeadline=rep(0,length(GOtermIDs)),
	MarkDetails=TRUE, Overwrite=TRUE, GOtermString=NULL,Remarkable=NULL,Pvalues=NULL,
	NrGenesInTerm=NULL,Expected = NULL, Observed = NULL, Importance = NULL, Up=NULL)

`Adj`	Adjacency matrix of GO terms where Adj[i,j]==1 iff i is parent of j.
`GOtermIDs`	GO term IDs, e.g. "GO:0008150".
`PlotFile`	Name of the output file. Extension determines the output format, one of png, eps, svg or pdf. Default output format: png.
`PlotDirectory`	Output directory. Default: getwd().
`Significant`	Terms with `Significant==1` are drawn in red, others white.
`IsHeadline`	Terms with `IsHeadline==1` are marked in yellow.
`MarkDetails`	Set TRUE if details of the dag should be coloured blue. Default: TRUE.
`Overwrite`	Set TRUE if files in `PlotDirectory` with same file name as `PlotFile` should be replaced by new file. Default: TRUE.
`GOtermString`	GO term strings, e.g "biological_process". If not given (NULL), GO term strings will be generated automatically.
`Remarkable`	Remarkable value of GO terms. See also `remarkableness`.
`Pvalues`	P-values of GO terms. Default: NULL.
`NrGenesInTerm`	The number of annotated genes for each GO term. Default: NULL
`Observed`	Number of observed annotations for each GO term. Default: NULL.
`Expected`	Number of statistically expected annotations for each GO term. Default: NULL.
`Importance`	Importance value of GO terms. Default: NULL.
`Up`	If there are more than the expected number of genes annotated to the GO term, `Up` is set to 1 else 0. GO terms where Up==1 are marked in red, others in green. Default: NULL