abundancePlot {PloGO2} | R Documentation |
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.
abundancePlot(res.list, log = FALSE, printLimit = 16, Group=NULL, Plot=FALSE, CountCutOff=3, ...)
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 |
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 |
D.Pascovici and J.Wu
See Also as processAnnotation
# 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() }