annotationPlot {PloGO2}

R Documentation

Function to summarize and plot extracted GO or pathway annotation

Description

Summarize the information from the GO or pathway annotation list into a table of counts and percentages, and possibly print a few images.

Usage

annotationPlot(res.list, percentages = FALSE, plot = TRUE, trimzero = FALSE, type=c("GO", "pathway"))
		

Arguments

res.list	The list of summarized annotation as generated by processAnnotation.
percentages	TRUE or FALSE.
plot	TRUE or FALSE: should plots be printed.
trimzero	TRUE or FALSE: should GO categories with no counts be removed. This is not really relevant when a small number of GO categories has been selected.
type	The type of annotation.

Value

counts	A matrix of counts, GO categories (rows) by samples (cols).
percentages	A matrix of percentages, GO categories (rows) by samples (cols).

Author(s)

D. Pascovici

See Also

See Also processAnnotation

Examples

## Not run: 
# get list of ID's
GOIDlist <- GOTermList("BP", 2)

# find existing files
dir <- system.file("files", package="PloGO2")
file.names <- paste(dir,c("00100.txt", "01111.txt", "10000.txt",
			"11111.txt","Control.txt"), sep="/")

# summarize annotation
res.list <- processAnnotation(file.names, GOIDlist)

annotationPlot(res.list, plot=FALSE)

## End(Not run)
# KEGG pathway
dir <- system.file("files", package="PloGO2")
fname <- file.path(dir,"PWFiles", c("red.txt", "blue.txt", "yellow.txt", "green.txt", "turquoise.txt") )
datafile <- file.path(dir,"Abundance_data.csv")

AnnotIDlist <- c("osa01100","osa01110","osa01230","osa00300","osa00860")
		
res.list <- processAnnotation(fname, AnnotIDlist,  data.file.name = datafile)

annotationPlot(res.list, plot=TRUE, type="pathway")

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