abundancePlot: Function to summarize and plot abundance information from an...

In PloGO2: Plot Gene Ontology and KEGG pathway Annotation and Abundance

Description

Generates one GO/pathway abundance plot for each file, and (provided the number of GO/pathway cateGO/pathwayries is reasonably small) also an abundance plot for each GO/pathway category across all files provided. The abundance values are *added* for all values in one category. Hence if the initial values represented percentages such as NSAF, the final values represent percentages of the respective category.

Usage

abundancePlot(res.list, log = FALSE, printLimit = 16, Group=NULL, Plot=FALSE, 
	CountCutOff=3, ...)

Arguments

res.list	The result returned by processAnnotation
log	TRUE/FALSE: use raw or log abundance data
printLimit	The most number of category to be plotted
Group	The groups
Plot	To plot or not
CountCutOff	The minimum number of proteins in a category for it to be plotted
...	Parameters to pass

Value

A list object, with the following values:

abundance	The abundance matrix
ag.mat	The aggregated abundance matrix
list.levelplots	A list of abundance levelplots trellis object
list.barplots	A list of abundance barcharts trellis object

Author(s)

D.Pascovici and J.Wu

See Also

See Also as processAnnotation

Examples

# get list of ID's
GOIDlist <- GOTermList("MF", 2)

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

# summarize annotation
res.list <- processAnnotation(file.names, GOIDlist, data.file.name = datafile)

abundance.res <- abundancePlot(res.list)

# Plot levelplots
list.levelplots <- abundance.res$list.levelplots

for(i in seq_along(list.levelplots)) {
	png(paste(names(list.levelplots)[i], ".png"), 2000, 4000, res=200)
	print(list.levelplots[[i]])
	dev.off()
}	


# KEGG pathway
path <- system.file("files", package="PloGO2")
file.names <- file.path(path,"PWFiles", c("AllData.txt","black.txt","blue.txt","brown.txt","green.txt",
	"red.txt","turquoise.txt") )
datafile <- file.path(path,"Abundance_data.csv")
Group <- names(read.csv(datafile))[-1]

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

abundance.res <- abundancePlot(res.list, Group=Group, Plot=TRUE)

# Plot levelplots
list.levelplots <- abundance.res$list.levelplots

for(i in seq_along(list.levelplots)) {
	png(paste(names(list.levelplots)[i], ".png"), 2000, 4000, res=200)
	print(list.levelplots[[i]])
	dev.off()
}	
# Plot barchats by categories
list.barplots <- abundance.res$list.barplots

for(i in seq_along(list.barplots)) {
	png(paste(names(list.barplots)[i], ".png"), 2000, 2000, res=200)
	print(list.barplots[[i]])
	dev.off()
	
}

PloGO2 documentation built on Nov. 8, 2020, 5:40 p.m.