ParseGOMFnPlot: Parse GO results using grep and plot

In mzinkgraf/treeGO: GO enrichment analysis for tree species

Description

This function creates a summary plot of GO$BP results by parsing GO results using grep and a list of search terms

Usage

ParseGOMFnPlot(grepList,GOresults, minT=0, Rorder=NULL,
             my_palette=colorRampPalette(c("white", "red"))(n = 8),
             main = "GO Enrichment",
             zlim = c(0,15), hlines=NULL )

Arguments

grepList	A list object where each value contains a group of search terms sperated by "|". The names and order values will be taken into account when plotting.
GOresults	A list containing multiple GO$MF objects from GOanalysis
minT	An integer specifying the minimum number of time a term must occur to be considered important. Default = 0
Rorder	Row order for how the results shoul dbe plotted
main	Title of the plot
zlim	Range specifying the p-values to be plotted
hlines	A "cumsum()" vector designating breaks for grouping modules
mypalette	Color palette used for heatmap

Value

Returns summary figure and summary table of results used to generate figure

Author(s)

Matthew Zinkgraf, [e-mail]

Examples

#generate some data
     set1 <- sample(Ptrichocarpa_210_annotation_primary$ATG)[1:2000]
     set2 <- sample(Ptrichocarpa_210_annotation_primary$ATG)[1:2000]

#calculate GO enrichment for MF
     GOresults<-list
     GOresults$set1<-atGOanalysis(set1,ontology="MF)
     GOresults$set2<-atGOanalysis(set2,ontology="MF)

#create search list
     grepList<-list()
     grepList$hormone<-"hormone|gibberelli|brassino|auxin"
     grepList$peroxisome <- "peroxi"
     grepList$localization <-"protein localization"

results<-ParseGOMFnPlot(grepList, GOresults)

mzinkgraf/treeGO documentation built on May 24, 2019, 6:10 a.m.