setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
source("./PAGER.R")

# pathFun is a function connected to PAGER api to perform hypergeometric test and retrieve enriched PAGs associated to a list of genes
# The input parameters are:
# 1.dir: the directory of output file.
# 2.filename: the name of the output file.
# 3.markers: a list of gene symbols.
# 4.type: a list of PAG types consisting of 'P', 'A' or 'G'
# 5.minSize: the allowed minimum size of PAG genes
# 6.maxSize: the allowed maximum size of PAG genes
# 7.similarity: the similarity score cutoff
# 8.overlap: the allowed minimum overlap genes
# 9.nCoCo: the minimum nCoCo score
# 10.pValue: p-value cutoff
# 11.FDR: false discovery rate 
# 12.source: a list of sources refered to 'http://discovery.informatics.uab.edu/PAGER/index.php/pages/help'
genes = c("BRCA1","BRCA2","RAD51","PGR")
PAG_result = pathFun(dir = "./", 
                 fileName = 'test.txt',  
                 genes,
                 type = "All", 
                 minSize = 2, 
                 maxSize = 5000, 
                 similarity = 0.05, 
                 overlap = 1, 
                 nCoCo = 0, 
                 pValue = 0.05, 
                 FDR = 0.05, 
                 Species = 'All', 
                 source = c('KEGG',"WikiPathway","BioCarta","MSigDB","NCI-Nature Curated","Reactome","Protein Lounge","Spike")
                 )
colnames(PAG_result)
head(PAG_result)
table(PAG_result$SOURCE)

# pathMember is a function connected to PAGER api to retrieve the membership of PAGs using a list of PAG IDs
# example:
PAG_member = pathMember(dir = "./",PAG_result$GS_ID)
head(PAG_member$data)

# pathInt is a function connected to PAGER api to retrieve the m-type relationships of PAGs using a list of PAG IDs
# example:
PAGint = pathInt(dir = './',PAG_result$GS_ID)
head(PAGint$data)

# pathReg is a function connected to PAGER api to retrieve the r-type relationships of PAGs using a list of PAG IDs
# example:
PAGreg=pathReg(dir = './',PAG_result$GS_ID)
head(PAGreg$data)

# pagRankedGene is a function connected to PAGER api to retrieve RP-ranked genes with RP-score of the given PAG_IDs
# example:
PAGRankedGenes=pagRankedGene(dir = './',PAG_result$GS_ID[1])
head(PAGRankedGenes$data)

# pagGeneInt is a function connected to PAGER api to retrieve gene interaction network
# example:
pagGeneInts=pagGeneInt(dir = './',PAG_result$GS_ID[1])
head(pagGeneInts$data)

# pagGeneReg is a function connected to PAGER api to retrieve gene regulatory network
# example:
pagGeneRegs=pagGeneReg(dir = './',PAG_result$GS_ID[1])
head(pagGeneRegs$data)


# path_NGSEA is a function connected to PAGER api to generate the network-based GSEA result
# example:
gene_df = data.frame(symbol = c("BRCA1","BRCA2","RAD51","PGR"), log2FoldChange = c(0.6,0.3,0.1,0.1))
pagInNetworkWGSEA=path_NGSEA(dir = './',gene_df,PAG_member)
head(pagInNetworkWGSEA$data)

# Cell Annotation 
CellInference=CellAnnotation(dir = './',
                             fileName = 'test_cell.txt', 
                             c('KLRB1','KLRC1','KLRD1','KLRF1'), 
                             minSize = 1, 
                             maxSize = 5000, 
                             similarity = 0, 
                             overlap = 1, 
                             pValue = 0.05,
                             FDR = 1, 
                             Species = 'All')
head(CellInference)