Nothing
ExcelToPloPathway <- function(fname, colName="Uniprot",
compareWithReference="none", DB.name="pathwayDB.csv",
data.file.name = "none",outFolder = "PloGO2Output")
{
wb <- (fname)
sheets <- names(openxlsx::loadWorkbook(wb))
data.list = lapply(sheets, FUN=function(s){ openxlsx::readWorkbook(wb, s) } )
id.list <- lapply(data.list, FUN=function(d){unique(d[,colName])})
# make output folder
if(!(outFolder %in% list.files())) dir.create(outFolder)
# get the annotation files
filespath <- genAnnotationFiles(fname,
colName=colName,
DB.name = DB.name, folder="PWFiles", outFolder)
# Run PloPathway
res = PloPathway(zipFile = "none",
reference = compareWithReference,
data.file.name = data.file.name,
datafile.ignore.cols = 1,
filesPath=filespath)
# Print results in temp file
printSummary(res, file=file.path(outFolder,"PloGO2Results.xlsx") )
sheets.plogo = names(loadWorkbook(file.path(outFolder,"PloGO2Results.xlsx")) )
if(!length(sheets) == (length(sheets.plogo)-1) ) warnings("the number of sheets in the input is different from PloGO2Results.xlsx")
# merge plopathway results and input file
list.mg = lapply(seq_len(length(sheets)), function(ii)
merge(readWorkbook(file.path(outFolder,"PloGO2Results.xlsx"), ii), data.list[[ii]], by.x="Protein", by.y=colName,
all=TRUE, sort=FALSE))
wb <- createWorkbook()
for(ii in seq_along(list.mg)) {
addWorksheet(wb, sheets[ii])
writeData(wb, sheets[ii], list.mg[[ii]])
}
addWorksheet(wb, sheets.plogo[length(sheets.plogo)])
writeData(wb, sheets.plogo[length(sheets.plogo)],
readWorkbook(file.path(outFolder,"PloGO2Results.xlsx"), length(sheets.plogo)) )
saveWorkbook(wb, file.path(outFolder,"PloGO2Results.xlsx"), overwrite=TRUE)
res
}
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