annotationPlot {PloGO2} | R Documentation |
Summarize the information from the GO or pathway annotation list into a table of counts and percentages, and possibly print a few images.
annotationPlot(res.list, percentages = FALSE, plot = TRUE, trimzero = FALSE, type=c("GO", "pathway"))
res.list |
The list of summarized annotation as generated by |
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. |
counts |
A matrix of counts, GO categories (rows) by samples (cols). |
percentages |
A matrix of percentages, GO categories (rows) by samples (cols). |
D. Pascovici
See Also processAnnotation
## 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")