## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----install_chunk, eval=FALSE------------------------------------------------
# 
# if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
# 
# BiocManager::install("EnrichDO")

## ----install_chunk2, eval=FALSE-----------------------------------------------
# 
# if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
# 
# library(devtools)
# devtools::install_github("liangcheng-hrbmu/EnrichDO")

## ----setup,results='hide'-----------------------------------------------------

library(EnrichDO)

## -----------------------------------------------------------------------------

Alzheimer<-read.delim(file.path(system.file("extdata", package="EnrichDO"), 
                                "Alzheimer_curated.csv"), header = FALSE)
input_example<-Alzheimer[,1]

## -----------------------------------------------------------------------------

demo.data<-c(1636,351,102,2932,3077,348,4137,54209,5663,5328,23621,3416,3553)

## ----eval=TRUE,results='hide',cache=TRUE,message=FALSE------------------------

weighted_demo_result<-doEnrich(interestGenes=demo.data)

## ----eval=FALSE---------------------------------------------------------------
# 
# weighted_demo_result<-doEnrich(interestGenes=demo.data,
#                         test="fisherTest",
#                         method="holm",
#                         m=1,
#                         minGsize=10,
#                         maxGsize=2000,
#                         delta=0.05,
#                         penalize=TRUE)

## ----echo=FALSE, results='hold'-----------------------------------------------
weighted_demo_result<-doEnrich(interestGenes=demo.data,test="fisherTest",method="holm",m=1,minGsize=10,
                        maxGsize=2000,delta=0.05,penalize=TRUE)

## -----------------------------------------------------------------------------

Tradition_demo_result<-doEnrich(demo.data, traditional=TRUE)

## ----eval=FALSE---------------------------------------------------------------
# 
# show(weighted_demo_result)

## ----echo=FALSE, results='hold'-----------------------------------------------

show(weighted_demo_result)

## -----------------------------------------------------------------------------

writeResult(EnrichResult = weighted_demo_result,file=file.path(tempdir(), "result.txt"), Q=1, P=1)

## ----fig.cap="bar plot",fig.align='center',fig.width=8,fig.height=6-----------

drawBarGraph(EnrichResult=weighted_demo_result, n=10, delta=0.05)

## ----fig.cap="point plot",fig.align='center',fig.width=8,fig.height=6---------

drawPointGraph(EnrichResult=weighted_demo_result, n=10, delta=0.05)

## ----fig.cap="tree plot",fig.align='center',fig.width=8,fig.height=6----------

drawGraphViz(EnrichResult=weighted_demo_result, n=10, numview=FALSE, pview=FALSE, labelfontsize=17)

## ----fig.cap="heatmap",fig.align='center',fig.width=8,fig.height=6------------

drawHeatmap(interestGenes=demo.data,
            EnrichResult=weighted_demo_result,
            gene_n=10,
            fontsize_row=8)

## ----fig.width=8,fig.height=6-------------------------------------------------
#Firstly, read the wrireResult output file,using the following two lines
data <- read.delim(file.path(system.file("examples", package="EnrichDO"), "result.txt"))
enrich <- convDraw(resultDO=data)

#then, Use the drawing function you need
drawGraphViz(enrich=enrich)    #Tree diagram

drawPointGraph(enrich=enrich, delta = 0.05)  #Bubble diagram

drawBarGraph(enrich=enrich, delta = 0.05)    #Bar plot

## ----session-info,cache = FALSE,echo=TRUE,message=TRUE,warning=FALSE----------

sessionInfo()

