## @knitr include=FALSE
library(DOSE)
library(GO.db)
library(org.Hs.eg.db)
library(pathview)
library(clusterProfiler)
library(knitr)
opts_chunk$set(tidy=TRUE,tidy.opts=list(keep.blank.line=FALSE, width.cutoff=50),out.truncate=80,out.lines=6,cache=TRUE,dev='pdf',include=TRUE,fig.width=6,fig.height=6,resolution=150)


## @knitr options,echo=FALSE
options(digits=3, width=80, prompt=" ", continue=" ")


## @knitr groupGO
require(DOSE)
data(geneList)
gene <- names(geneList)[abs(geneList) > 2]
head(gene)
ggo <- groupGO(gene=gene, organism="human",
				ont="BP", level=3, readable=TRUE)
head(summary(ggo))


## @knitr enrichGO
ego <- enrichGO(gene=gene,
				universe = names(geneList),
              organism="human",
              ont="CC",
              pvalueCutoff=0.01,
              readable=TRUE)
head(summary(ego))


## @knitr enrichKEGG
kk <- enrichKEGG(gene=gene,
                organism="human",
                pvalueCutoff=0.01,
                readable=TRUE)
head(summary(kk))


## @knitr barplot, fig.height=5, fig.width=6
barplot(ggo, drop=TRUE, showCategory=12)


## @knitr barplot-enrich, fig.height=5, fig.width=8
barplot(ego, showCategory=8)


## @knitr cnetplot, fig.height=14, fig.width=14
cnetplot(ego, categorySize="pvalue", foldChange=geneList)


## @knitr cnetplot-KEGG, fig.height=14, fig.width=14
cnetplot(kk, categorySize="geneNum", foldChange=geneList)


## @knitr viewKEGG
require(pathview)
hsa04110 <- pathview(gene.data=geneList, pathway.id="hsa04110", species="hsa", limit=list(gene=max(abs(geneList)), cpd=1))


## @knitr compareCluster, fig.height=8, fig.width=8
data(gcSample)
ck <- compareCluster(geneCluster=gcSample, fun="enrichKEGG")
plot(ck)


## @knitr sessInfo, results='asis', echo=FALSE
toLatex(sessionInfo())