showSigNodes: Drawing the GO DAG structure of statistically significant...

In GOFunction: GO-function: deriving biologcially relevant functions from statistically significant functions

Description

According to the GO DAG structure created by the "createGODAG" function, this function draws the corresponding plot.

Arguments

DAG	DAG is a object of 'graphNEL' class which contains the GO DAG structure of statistically significant GO terms.
sigTerm	sigTerm is the GO terms found by enrichmentFunction function.
sigTerm_Local	sigTerm_Local is the remained statistically signifcant terms after treating local redundancy.
sigTerm_Global	sigTerm_Glocal is the remained statistically signifcant terms after treating global redundancy.
dagTermInfo	dagTermInfo is the information of all related GO terms in GO DAG.
bmpSize	bmpSize is the width and height of the plot of GO DAG for all statistically significant terms. GO-function set the default width and height of the plot as 2000 pixels in order to clearly show the GO DAG structure. If the GO DAG is very complexity, the user should increase bmpSize. Note: If there is an error at the step of "bmp(filename, width = 2000, ..." when running GO-function, the user should decrease bmpSize.
filename	filename is the name of the files saving the table and the GO DAG of all statistically significant terms.

Value

This function saves the structure of GO DAG for all statistic significant terms into a plot (e.g. "sigTerm.bmp") in the current working folder. In this plot, "circle" represents terms removed after local redundancy treatment, "box" represents terms removed after treating global redundancy and "rectangle" represents the remained terms with evidence that their significance should not be simply due to the overlapping genes. The dfferent color shades represent the adjusted p values of the terms.

Author(s)

Jing Wang

See Also

GOFunction enrichmentFunction localRedundancy globalRedundancy createGODAG

GOFunction documentation built on April 28, 2020, 6:55 p.m.