plotGOgraph: Function to draw and save gene ontology DAG.

In JornLotsch/dbtORA: Overrepresentation Analysis

Description

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

Usage

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)

Arguments

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.
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

Value

PlotFile in PlotDirectory with DAG of input GO terms.

Author(s)

CL

JornLotsch/dbtORA documentation built on Dec. 31, 2020, 2:05 p.m.