graphCell: Makes a GO graph highlighting the GO terms in the selected...

In mvGST: Multivariate and directional gene set testing

Description

graphCell relies on tools in the Rgraphviz package. graphCell uses pickOut to get the GO terms in a specific cell of the results table. A GO graph is created from those GO terms, and can be interactive if desired. Also, if desired, a legend showing the names of the GO terms can be printed. If the graph is interactive, use esc to end interaction with graph.

Usage

graphCell(object, row, col = 1, set, ontology = "BP", interact = TRUE, 
          legend.pos = "bottomleft", print.legend = TRUE,
		  use.col="red", bg.col = "grey80")

Arguments

object	A mvGST object with a final results.table
row	The row of the desired cell.
col	The column of the desired cell. Column refers to the levels of Var2, if Var2 was used. It is the number of the column after the 1, 0, -1 columns that show the profiles. Default value is 1.
set	Optional argument that is a data frame with the first column containing the GO ID's that should be used to make the GO graph. The data frame returned by pickOut can be used.
ontology	The ontology, within Gene Ontology, that should be used ("BP", "MF", "CC").
interact	Indicates whether or not the graph should be interactive. If interactive, use esc to end interaction with graph.
legend.pos	If interactive, indicates the desired position of the legend that shows name and GO ID of selected node.
print.legend	Indicates if the legend should also be printed separately, showing GO names of all nodes.
use.col	Color to highlight the nodes representing gene sets of interest in the resulting graph.
bg.col	Color to use for the "background" in the graph when focusing on the gene sets of interest. This is the color used for the border of all nodes, the labels of all nodes NOT representing gene sets of interest, and all edges.

Details

To access the tutorial document for this package, type in R: vignette("mvGST")

Value

Invisibly returns NULL.

Author(s)

John R. Stevens and Dennis S. Mecham

References

Stevens, J. R., and Isom, S. C., 2012. "Gene set testing to characterize multivariately differentially expressed genes." Conference on Applied Statistics in Agriculture Proceedings, 24, pp. 125-137.

Mecham, D. S. (2014) "mvGST: Multivariate and Directional Gene Set Testing". MS Project, Utah State University, Department of Mathematics and Statistics. http://digitalcommons.usu.edu/gradreports/382/

Examples

data(mvGSTsamples)
# object obatoclax.mvGST returned by profileTable
obatoclax.mvGST

# plots a GO Graph highlighting the GO ID's from the cell 
# in the fifth row and first column (the column for 
# cell line RS4) of the results.table of the object 
# returned by profileTable
graphCell(obatoclax.mvGST, 5, 1, ontology = "BP", interact = FALSE)

# See package vignette for larger examples with discussion: 
#    vignette("mvGST")

mvGST documentation built on March 18, 2018, 2:35 p.m.