R/SingleRepReport.R
In wzthu/wzzw: An Easy-to-use Systematic pipeline for ATACseq data analysis
setClass(Class = "SingleRepReport",
contains = "ATACProc"
)
setMethod(
f = "init",
signature = "SingleRepReport",
definition = function(.Object,prevSteps = list(),...){
allparam <- list(...)
htmlOutput <- allparam[["htmlOutput"]]
param(.Object)[["createHTML"]] <- allparam[["createHTML"]]
if(is.null(htmlOutput)){
output(.Object)$htmlOutput <- getStepWorkDir(.Object, filename = "Report.html")
}else{
output(.Object)$htmlOutput <- getStepWorkDir(.Object, filename = htmlOutput)
}
output(.Object)$reportData <- getStepWorkDir(.Object, filename = "ReportData")
.Object
}
)
#' @importFrom rmarkdown render
#' @importFrom pipeFrame stepType
setMethod(
f = "processing",
signature = "SingleRepReport",
definition = function(.Object, ...){
htmlOutput <- output(.Object)[["htmlOutput"]]
prevSteps <- list(...)[["prevSteps"]]
createHTML <- param(.Object)[["createHTML"]]
dir.create(output(.Object)$reportData)
sumDir <- file.path(output(.Object)$reportData,"SummaryInfo")
dir.create(sumDir)
rsDir <- file.path(output(.Object)$reportData,"ResultData")
dir.create(rsDir)
prevStepsType <- lapply(prevSteps, function(step){
if(is.null(step)){
return(paste0("NULL", sample(1:100,1)))
}
st <- stepType(step)
return(st)
})
names(prevSteps) <- unlist(prevStepsType)
wholesummary <- NULL
filtstat <- NULL
unzipAndMerge <- prevSteps[["UnzipAndMerge"]]
renamer <- prevSteps[["Renamer"]]
removeAdapter <- prevSteps[["RemoveAdapter"]]
bowtie2Mapping <- prevSteps[["Bowtie2Mapping"]]
libComplexQC <- prevSteps[["LibComplexQC"]]
sam2Bed <- prevSteps[["SamToBed"]]
if(is.null(sam2Bed)){
sam2Bed <- prevSteps[["BamToBed"]]
}
bedToBigWig <- prevSteps[["BedToBigWig"]]
tssqc100 <- prevSteps[["TSSQCNFR"]]
tssqc180_247 <- prevSteps[["TSSQCneucleosome"]]
fragLenDistr <- prevSteps[["FragLenDistr"]]
peakCalling <- prevSteps[["PeakCallingFseq"]]
DHSQC <- prevSteps[["PeakQCDHS"]]
blacklistQC <- prevSteps[["PeakQCblacklist"]]
fripQC <- prevSteps[["FRiPQC"]]
shortBed <- prevSteps[["BedUtils"]]
Peakanno <- prevSteps[["RPeakAnno"]]
goAna <- prevSteps[["RGo"]]
output_motifscan <- prevSteps[["RMotifScan"]]
cs_output <- prevSteps[["CutSitePre"]]
footprint <- prevSteps[["CutSiteCountR"]]
atacQC <- prevSteps[["FastQC"]]
if(property(.Object)$singleEnd && !property(.Object)$interleave){
wholesummary <- data.frame(Item=c("Sequence Files Type",
"Original total reads",
"-- Reads after adapter removing (ratio)",
"-- -- Total mapped reads (ratio of original reads)",
"-- -- -- Unique locations mapped uniquely by reads",
"-- -- -- Uniquely mappable reads",
"-- -- -- Non-Redundant Fraction (NRF)",
"-- -- -- Locations with only 1 reads mapping uniquely",
"-- -- -- Locations with only 2 reads mapping uniquely",
"-- -- -- PCR Bottlenecking Coefficients 1 (PBC1)",
"-- -- -- PCR Bottlenecking Coefficients 2 (PBC2)",
"-- -- -- Non-mitochondrial reads (ratio)",
"-- -- -- -- Unique mapped reads (ratio)",
"-- -- -- -- -- Duplicate removed reads (final for use)",
"-- -- -- -- -- -- -- Total peaks",
"-- -- -- -- -- -- -- Peaks overlaped with union DHS ratio",
"-- -- -- -- -- -- -- Peaks overlaped with blacklist ratio",
"-- -- -- -- -- -- Fraction of reads in peaks (FRiP)"),
Value=c(report(unzipAndMerge)[["seqtype"]],
getVMShow(report(removeAdapter)[["statisticslist"]][[1]]),
getVMRShow(as.integer(report(removeAdapter)[["statisticslist"]][["Number of retained reads"]]) /
report(unzipAndMerge)[["frag"]],
report(removeAdapter)[["statisticslist"]][[1]]),
getVMRShow(report(sam2Bed)[["total"]],
report(removeAdapter)[["statisticslist"]][[1]]),
getVMShow(report(libComplexQC)[["total"]]),
#sam2Bed$report("non-mitochondrial-multimap"]]),
getVMShow(report(libComplexQC)[["nonMultimap"]]),
#getf(libComplexQC$report("NRF"]]),
getRshow(report(libComplexQC)[["total"]],
report(libComplexQC)[["nonMultimap"]]),
getVMShow(report(libComplexQC)[["one"]]),
#sam2Bed$report("non-mitochondrial-multimap"]]),
getVMShow(report(libComplexQC)[["two"]]),
#sam2Bed$report("non-mitochondrial-multimap"]]),
#getf(libComplexQC$report("PBC1"]]),
getRshow(report(libComplexQC)[["one"]],
report(libComplexQC)[["total"]]),
#getf(libComplexQC$report("PBC2"]]),
getRshow(report(libComplexQC)[["one"]],
report(libComplexQC)[["two"]]),
getVMRShow(report(sam2Bed)[["non-mitochondrial"]],
report(sam2Bed)[["total"]]),
getVMRShow(report(sam2Bed)[["non-mitochondrial-multimap"]],
report(sam2Bed)[["total"]]),
getVMRShow(report(sam2Bed)[["save"]],
report(sam2Bed)[["total"]]),
sprintf("%d",as.numeric(report(fripQC)[["totalPeaks"]])),
ifelse(is.null(DHSQC),"NA",getPer(report(DHSQC)[["qcbedRate"]])),
ifelse(is.null(blacklistQC),"NA",getPer(report(blacklistQC)[["qcbedRate"]])),
getPer(report(fripQC)[["FRiP"]]))
,
`Reference`=c("SE / PE",
"",
">99%",
">95%",
"",
"",
">0.7",
"",
"",
">0.7",
">3",
">70%",
"",
">25M",
"",
"",
"",
""
)
#`Annotation`=c()
)
filtstat = data.frame(
Item=c("Original total reads",
"Reads after adapter removing (ratio)",
"Total mapped reads (ratio of original reads)",
"-- Non-mitochondrial reads (ratio)",
"-- -- Unique mapped reads (ratio)",
"-- -- -- Duplicate removed reads (ratio final for use)"
),
Value=c(getVMShow(report(removeAdapter)[["statisticslist"]][[1]],TRUE),
getVMRShow(as.integer(report(removeAdapter)[["statisticslist"]][["Number of retained reads"]])/report(unzipAndMerge)[["frag"]],
report(removeAdapter)[["statisticslist"]][[1]],TRUE),
getVMRShow(report(sam2Bed)[["total"]],
report(removeAdapter)[["statisticslist"]][[1]],TRUE),
getVMRShow(report(sam2Bed)[["non-mitochondrial"]],
report(sam2Bed)[["total"]],TRUE),
getVMRShow(report(sam2Bed)[["non-mitochondrial-multimap"]],
report(sam2Bed)[["total"]],TRUE),
getVMRShow(report(sam2Bed)[["save"]],
report(sam2Bed)[["total"]],TRUE)
),
`Reference`=c("",
">99%",
">95%",
">70%",
">60%",
">25M,>60%"
)
)
}else{
wholesummary = data.frame(Item=c("Sequence Files Type",
"Original total reads",
"-- Reads after adapter removing (ratio)",
"-- -- Total mapped reads (ratio of original reads)",
"-- -- -- Unique locations mapped uniquely by reads",
"-- -- -- Uniquely mappable reads",
"-- -- -- Non-Redundant Fraction (NRF)",
"-- -- -- Locations with only 1 reads mapping uniquely",
"-- -- -- Locations with only 2 reads mapping uniquely",
"-- -- -- PCR Bottlenecking Coefficients 1 (PBC1)",
"-- -- -- PCR Bottlenecking Coefficients 2 (PBC2)",
"-- -- -- Non-mitochondrial reads (ratio)",
"-- -- -- -- Unique mapped reads (ratio)",
"-- -- -- -- -- Duplicate removed reads (final for use)",
#"---- -- -- -- -- Transcription start site (TSS) enrichment",
"-- -- -- -- -- -- Nucleosome free reads (<100bp)",
"-- -- -- -- -- -- -- Total peaks",
"-- -- -- -- -- -- -- Peaks overlaped with union DHS ratio",
"-- -- -- -- -- -- -- Peaks overlaped with blacklist ratio",
"-- -- -- -- -- -- Fraction of reads in peaks (FRiP)"),
Value=c(report(unzipAndMerge)[["seqtype"]],
getVMShow(report(removeAdapter)[["statisticslist"]][[1]]),
getVMRShow(as.integer(report(removeAdapter)[["statisticslist"]][["Number of retained reads"]])/report(unzipAndMerge)[["frag"]],
report(removeAdapter)[["statisticslist"]][[1]]),
getVMRShow(report(sam2Bed)[["total"]],
report(removeAdapter)[["statisticslist"]][[1]]),
getVMShow(report(libComplexQC)[["total"]]),
#sam2Bed$report("non-mitochondrial-multimap"]]),
getVMShow(report(libComplexQC)[["nonMultimap"]]),
#getf(libComplexQC$report("NRF"]]),
getRshow(report(libComplexQC)[["total"]],
report(libComplexQC)[["nonMultimap"]]),
getVMShow(report(libComplexQC)[["one"]]),
#sam2Bed$report("non-mitochondrial-multimap"]]),
getVMShow(report(libComplexQC)[["two"]]),
#sam2Bed$report("non-mitochondrial-multimap"]]),
#getf(libComplexQC$report("PBC1"]]),
getRshow(report(libComplexQC)[["one"]],
report(libComplexQC)[["total"]]),
#getf(libComplexQC$report("PBC2"]]),
getRshow(report(libComplexQC)[["one"]],
report(libComplexQC)[["two"]]),
getVMRShow(report(sam2Bed)[["non-mitochondrial"]],
report(sam2Bed)[["total"]]),
getVMRShow(report(sam2Bed)[["non-mitochondrial-multimap"]],
report(sam2Bed)[["total"]]),
getVMRShow(report(sam2Bed)[["save"]],
report(sam2Bed)[["total"]]),
#"",
getVMRShow(report(shortBed)[["save"]],
report(shortBed)[["total"]]),
sprintf("%d",as.numeric(report(fripQC)[["totalPeaks"]])),
ifelse(is.null(DHSQC),"NA",getPer(report(DHSQC)[["qcbedRate"]])),
ifelse(is.null(blacklistQC),"NA",getPer(report(blacklistQC)[["qcbedRate"]])),
getPer(report(fripQC)[["FRiP"]]))
,
`Reference`=c("SE / PE",
"",
">99%",
">95%",
"",
"",
">0.7",
"",
"",
">0.7",
">3",
">70%",
"",
">25M",
#"",
"",
"",
"",
"",
""
)
#`Annotation`=c()
)
filtstat = data.frame(
Item=c("Original total reads",
"Reads after adapter removing (ratio)",
"Total mapped reads (ratio of original reads)",
"-- Non-mitochondrial reads (ratio)",
"-- -- Unique mapped reads (ratio)",
"-- -- -- Duplicate removed reads (ratio final for use)"
),
Value=c(getVMShow(report(removeAdapter)[["statisticslist"]][[1]],TRUE),
getVMRShow(as.integer(report(removeAdapter)[["statisticslist"]][["Number of retained reads"]])/report(unzipAndMerge)[["frag"]],
report(removeAdapter)[["statisticslist"]][[1]],TRUE),
getVMRShow(report(sam2Bed)[["total"]],
report(removeAdapter)[["statisticslist"]][[1]],TRUE),
getVMRShow(report(sam2Bed)[["non-mitochondrial"]],
report(sam2Bed)[["total"]],TRUE),
getVMRShow(report(sam2Bed)[["non-mitochondrial-multimap"]],
report(sam2Bed)[["total"]],TRUE),
getVMRShow(report(sam2Bed)[["save"]],
report(sam2Bed)[["total"]],TRUE)
),
`Reference`=c("",
">99%",
">95%",
">70%",
">60%",
">25M,>60%"
)
)
}
saveRDS(list(prevSteps = prevSteps,
wholesummary = wholesummary,
filtstat = filtstat),
file = file.path(sumDir,"suminfo.rds"))
saveConfig(file.path(sumDir,"config.rds"))
reportmkd <- getStepWorkDir(.Object = .Object, filename = "Report.Rmd")
reportmkd1 <- getStepWorkDir(.Object = .Object, filename = "Report.code.Rmd")
file.copy(from = system.file(package = "esATAC", "extdata","Report.Rmd"),
to = reportmkd,overwrite = TRUE)
# file.copy(from = system.file(package = "enrichTF", "extdata","Report.code.Rmd"),
# to = reportmkd1,overwrite = TRUE)
if(createHTML){
render(reportmkd)
}else{
writeLines('html is not generated', htmlOutput)
}
# render(reportmkd1, quiet = TRUE)
.Object
}
)
setMethod(
f = "genReport",
signature = "SingleRepReport",
definition = function(.Object, ...){
.Object
}
)
#' @name SingleRepReport
#' @importFrom rtracklayer import
#' @importFrom rtracklayer import.bed
#' @title Final report for single group of regions
#' @description
#' When user call all steps in the pipeline, the final report can be generated.
#' @param prevStep \code{\link{Step-class}} object scalar.
#' Any steps object in this package is acceptable when the pipeline is ready.
#' @param htmlOutput \code{Character} scalar.
#' HTML report file directory
#' Default: NULL ("Report.html")
#' @param createHTML \code{Logical} scalar.
#' If create HTML file. Default: TRUE.
#' This parameter needs to be set FALSE
#' when pandoc or other dependence softwares are not available for rmarkdown package.
#' @param ... Additional arguments, currently unused.
#' @details
#' The report is HTML format. All link in HTML file is the relative directory
#' in report step folder and other step folder
#' If user want to move HTML file and keep all link access available,
#' they should move the whole pipeline folder at the same time.
#' @return An invisible \code{\link{ATACProc-class}}
#' object (\code{\link{Step-class}} based) scalar for downstream analysis.
#' @author Zheng Wei
#' @seealso
#' \code{\link{atacPipe}}
setGeneric("atacSingleRepReport",
function(prevStep, htmlOutput = NULL, createHTML = TRUE,...)
standardGeneric("atacSingleRepReport"))
#' @rdname SingleRepReport
#' @aliases atacSingleRepReport
#' @export
setMethod(
f = "atacSingleRepReport",
signature = "Step",
definition = function(prevStep, htmlOutput = NULL, createHTML = TRUE, ...){
allpara <- c(list(Class = "SingleRepReport",
prevSteps = list(prevStep), isReportStep = TRUE),
as.list(environment()),list(...))
step <- do.call(new,allpara)
invisible(step)
}
)
wzthu/wzzw documentation built on Aug. 13, 2022, 7:11 a.m.
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setClass(Class = "SingleRepReport",
contains = "ATACProc"
)
setMethod(
f = "init",
signature = "SingleRepReport",
definition = function(.Object,prevSteps = list(),...){
allparam <- list(...)
htmlOutput <- allparam[["htmlOutput"]]
param(.Object)[["createHTML"]] <- allparam[["createHTML"]]
if(is.null(htmlOutput)){
output(.Object)$htmlOutput <- getStepWorkDir(.Object, filename = "Report.html")
}else{
output(.Object)$htmlOutput <- getStepWorkDir(.Object, filename = htmlOutput)
}
output(.Object)$reportData <- getStepWorkDir(.Object, filename = "ReportData")
.Object
}
)
#' @importFrom rmarkdown render
#' @importFrom pipeFrame stepType
setMethod(
f = "processing",
signature = "SingleRepReport",
definition = function(.Object, ...){
htmlOutput <- output(.Object)[["htmlOutput"]]
prevSteps <- list(...)[["prevSteps"]]
createHTML <- param(.Object)[["createHTML"]]
dir.create(output(.Object)$reportData)
sumDir <- file.path(output(.Object)$reportData,"SummaryInfo")
dir.create(sumDir)
rsDir <- file.path(output(.Object)$reportData,"ResultData")
dir.create(rsDir)
prevStepsType <- lapply(prevSteps, function(step){
if(is.null(step)){
return(paste0("NULL", sample(1:100,1)))
}
st <- stepType(step)
return(st)
})
names(prevSteps) <- unlist(prevStepsType)
wholesummary <- NULL
filtstat <- NULL
unzipAndMerge <- prevSteps[["UnzipAndMerge"]]
renamer <- prevSteps[["Renamer"]]
removeAdapter <- prevSteps[["RemoveAdapter"]]
bowtie2Mapping <- prevSteps[["Bowtie2Mapping"]]
libComplexQC <- prevSteps[["LibComplexQC"]]
sam2Bed <- prevSteps[["SamToBed"]]
if(is.null(sam2Bed)){
sam2Bed <- prevSteps[["BamToBed"]]
}
bedToBigWig <- prevSteps[["BedToBigWig"]]
tssqc100 <- prevSteps[["TSSQCNFR"]]
tssqc180_247 <- prevSteps[["TSSQCneucleosome"]]
fragLenDistr <- prevSteps[["FragLenDistr"]]
peakCalling <- prevSteps[["PeakCallingFseq"]]
DHSQC <- prevSteps[["PeakQCDHS"]]
blacklistQC <- prevSteps[["PeakQCblacklist"]]
fripQC <- prevSteps[["FRiPQC"]]
shortBed <- prevSteps[["BedUtils"]]
Peakanno <- prevSteps[["RPeakAnno"]]
goAna <- prevSteps[["RGo"]]
output_motifscan <- prevSteps[["RMotifScan"]]
cs_output <- prevSteps[["CutSitePre"]]
footprint <- prevSteps[["CutSiteCountR"]]
atacQC <- prevSteps[["FastQC"]]
if(property(.Object)$singleEnd && !property(.Object)$interleave){
wholesummary <- data.frame(Item=c("Sequence Files Type",
"Original total reads",
"-- Reads after adapter removing (ratio)",
"-- -- Total mapped reads (ratio of original reads)",
"-- -- -- Unique locations mapped uniquely by reads",
"-- -- -- Uniquely mappable reads",
"-- -- -- Non-Redundant Fraction (NRF)",
"-- -- -- Locations with only 1 reads mapping uniquely",
"-- -- -- Locations with only 2 reads mapping uniquely",
"-- -- -- PCR Bottlenecking Coefficients 1 (PBC1)",
"-- -- -- PCR Bottlenecking Coefficients 2 (PBC2)",
"-- -- -- Non-mitochondrial reads (ratio)",
"-- -- -- -- Unique mapped reads (ratio)",
"-- -- -- -- -- Duplicate removed reads (final for use)",
"-- -- -- -- -- -- -- Total peaks",
"-- -- -- -- -- -- -- Peaks overlaped with union DHS ratio",
"-- -- -- -- -- -- -- Peaks overlaped with blacklist ratio",
"-- -- -- -- -- -- Fraction of reads in peaks (FRiP)"),
Value=c(report(unzipAndMerge)[["seqtype"]],
getVMShow(report(removeAdapter)[["statisticslist"]][[1]]),
getVMRShow(as.integer(report(removeAdapter)[["statisticslist"]][["Number of retained reads"]]) /
report(unzipAndMerge)[["frag"]],
report(removeAdapter)[["statisticslist"]][[1]]),
getVMRShow(report(sam2Bed)[["total"]],
report(removeAdapter)[["statisticslist"]][[1]]),
getVMShow(report(libComplexQC)[["total"]]),
#sam2Bed$report("non-mitochondrial-multimap"]]),
getVMShow(report(libComplexQC)[["nonMultimap"]]),
#getf(libComplexQC$report("NRF"]]),
getRshow(report(libComplexQC)[["total"]],
report(libComplexQC)[["nonMultimap"]]),
getVMShow(report(libComplexQC)[["one"]]),
#sam2Bed$report("non-mitochondrial-multimap"]]),
getVMShow(report(libComplexQC)[["two"]]),
#sam2Bed$report("non-mitochondrial-multimap"]]),
#getf(libComplexQC$report("PBC1"]]),
getRshow(report(libComplexQC)[["one"]],
report(libComplexQC)[["total"]]),
#getf(libComplexQC$report("PBC2"]]),
getRshow(report(libComplexQC)[["one"]],
report(libComplexQC)[["two"]]),
getVMRShow(report(sam2Bed)[["non-mitochondrial"]],
report(sam2Bed)[["total"]]),
getVMRShow(report(sam2Bed)[["non-mitochondrial-multimap"]],
report(sam2Bed)[["total"]]),
getVMRShow(report(sam2Bed)[["save"]],
report(sam2Bed)[["total"]]),
sprintf("%d",as.numeric(report(fripQC)[["totalPeaks"]])),
ifelse(is.null(DHSQC),"NA",getPer(report(DHSQC)[["qcbedRate"]])),
ifelse(is.null(blacklistQC),"NA",getPer(report(blacklistQC)[["qcbedRate"]])),
getPer(report(fripQC)[["FRiP"]]))
,
`Reference`=c("SE / PE",
"",
">99%",
">95%",
"",
"",
">0.7",
"",
"",
">0.7",
">3",
">70%",
"",
">25M",
"",
"",
"",
""
)
#`Annotation`=c()
)
filtstat = data.frame(
Item=c("Original total reads",
"Reads after adapter removing (ratio)",
"Total mapped reads (ratio of original reads)",
"-- Non-mitochondrial reads (ratio)",
"-- -- Unique mapped reads (ratio)",
"-- -- -- Duplicate removed reads (ratio final for use)"
),
Value=c(getVMShow(report(removeAdapter)[["statisticslist"]][[1]],TRUE),
getVMRShow(as.integer(report(removeAdapter)[["statisticslist"]][["Number of retained reads"]])/report(unzipAndMerge)[["frag"]],
report(removeAdapter)[["statisticslist"]][[1]],TRUE),
getVMRShow(report(sam2Bed)[["total"]],
report(removeAdapter)[["statisticslist"]][[1]],TRUE),
getVMRShow(report(sam2Bed)[["non-mitochondrial"]],
report(sam2Bed)[["total"]],TRUE),
getVMRShow(report(sam2Bed)[["non-mitochondrial-multimap"]],
report(sam2Bed)[["total"]],TRUE),
getVMRShow(report(sam2Bed)[["save"]],
report(sam2Bed)[["total"]],TRUE)
),
`Reference`=c("",
">99%",
">95%",
">70%",
">60%",
">25M,>60%"
)
)
}else{
wholesummary = data.frame(Item=c("Sequence Files Type",
"Original total reads",
"-- Reads after adapter removing (ratio)",
"-- -- Total mapped reads (ratio of original reads)",
"-- -- -- Unique locations mapped uniquely by reads",
"-- -- -- Uniquely mappable reads",
"-- -- -- Non-Redundant Fraction (NRF)",
"-- -- -- Locations with only 1 reads mapping uniquely",
"-- -- -- Locations with only 2 reads mapping uniquely",
"-- -- -- PCR Bottlenecking Coefficients 1 (PBC1)",
"-- -- -- PCR Bottlenecking Coefficients 2 (PBC2)",
"-- -- -- Non-mitochondrial reads (ratio)",
"-- -- -- -- Unique mapped reads (ratio)",
"-- -- -- -- -- Duplicate removed reads (final for use)",
#"---- -- -- -- -- Transcription start site (TSS) enrichment",
"-- -- -- -- -- -- Nucleosome free reads (<100bp)",
"-- -- -- -- -- -- -- Total peaks",
"-- -- -- -- -- -- -- Peaks overlaped with union DHS ratio",
"-- -- -- -- -- -- -- Peaks overlaped with blacklist ratio",
"-- -- -- -- -- -- Fraction of reads in peaks (FRiP)"),
Value=c(report(unzipAndMerge)[["seqtype"]],
getVMShow(report(removeAdapter)[["statisticslist"]][[1]]),
getVMRShow(as.integer(report(removeAdapter)[["statisticslist"]][["Number of retained reads"]])/report(unzipAndMerge)[["frag"]],
report(removeAdapter)[["statisticslist"]][[1]]),
getVMRShow(report(sam2Bed)[["total"]],
report(removeAdapter)[["statisticslist"]][[1]]),
getVMShow(report(libComplexQC)[["total"]]),
#sam2Bed$report("non-mitochondrial-multimap"]]),
getVMShow(report(libComplexQC)[["nonMultimap"]]),
#getf(libComplexQC$report("NRF"]]),
getRshow(report(libComplexQC)[["total"]],
report(libComplexQC)[["nonMultimap"]]),
getVMShow(report(libComplexQC)[["one"]]),
#sam2Bed$report("non-mitochondrial-multimap"]]),
getVMShow(report(libComplexQC)[["two"]]),
#sam2Bed$report("non-mitochondrial-multimap"]]),
#getf(libComplexQC$report("PBC1"]]),
getRshow(report(libComplexQC)[["one"]],
report(libComplexQC)[["total"]]),
#getf(libComplexQC$report("PBC2"]]),
getRshow(report(libComplexQC)[["one"]],
report(libComplexQC)[["two"]]),
getVMRShow(report(sam2Bed)[["non-mitochondrial"]],
report(sam2Bed)[["total"]]),
getVMRShow(report(sam2Bed)[["non-mitochondrial-multimap"]],
report(sam2Bed)[["total"]]),
getVMRShow(report(sam2Bed)[["save"]],
report(sam2Bed)[["total"]]),
#"",
getVMRShow(report(shortBed)[["save"]],
report(shortBed)[["total"]]),
sprintf("%d",as.numeric(report(fripQC)[["totalPeaks"]])),
ifelse(is.null(DHSQC),"NA",getPer(report(DHSQC)[["qcbedRate"]])),
ifelse(is.null(blacklistQC),"NA",getPer(report(blacklistQC)[["qcbedRate"]])),
getPer(report(fripQC)[["FRiP"]]))
,
`Reference`=c("SE / PE",
"",
">99%",
">95%",
"",
"",
">0.7",
"",
"",
">0.7",
">3",
">70%",
"",
">25M",
#"",
"",
"",
"",
"",
""
)
#`Annotation`=c()
)
filtstat = data.frame(
Item=c("Original total reads",
"Reads after adapter removing (ratio)",
"Total mapped reads (ratio of original reads)",
"-- Non-mitochondrial reads (ratio)",
"-- -- Unique mapped reads (ratio)",
"-- -- -- Duplicate removed reads (ratio final for use)"
),
Value=c(getVMShow(report(removeAdapter)[["statisticslist"]][[1]],TRUE),
getVMRShow(as.integer(report(removeAdapter)[["statisticslist"]][["Number of retained reads"]])/report(unzipAndMerge)[["frag"]],
report(removeAdapter)[["statisticslist"]][[1]],TRUE),
getVMRShow(report(sam2Bed)[["total"]],
report(removeAdapter)[["statisticslist"]][[1]],TRUE),
getVMRShow(report(sam2Bed)[["non-mitochondrial"]],
report(sam2Bed)[["total"]],TRUE),
getVMRShow(report(sam2Bed)[["non-mitochondrial-multimap"]],
report(sam2Bed)[["total"]],TRUE),
getVMRShow(report(sam2Bed)[["save"]],
report(sam2Bed)[["total"]],TRUE)
),
`Reference`=c("",
">99%",
">95%",
">70%",
">60%",
">25M,>60%"
)
)
}
saveRDS(list(prevSteps = prevSteps,
wholesummary = wholesummary,
filtstat = filtstat),
file = file.path(sumDir,"suminfo.rds"))
saveConfig(file.path(sumDir,"config.rds"))
reportmkd <- getStepWorkDir(.Object = .Object, filename = "Report.Rmd")
reportmkd1 <- getStepWorkDir(.Object = .Object, filename = "Report.code.Rmd")
file.copy(from = system.file(package = "esATAC", "extdata","Report.Rmd"),
to = reportmkd,overwrite = TRUE)
# file.copy(from = system.file(package = "enrichTF", "extdata","Report.code.Rmd"),
# to = reportmkd1,overwrite = TRUE)
if(createHTML){
render(reportmkd)
}else{
writeLines('html is not generated', htmlOutput)
}
# render(reportmkd1, quiet = TRUE)
.Object
}
)
setMethod(
f = "genReport",
signature = "SingleRepReport",
definition = function(.Object, ...){
.Object
}
)
#' @name SingleRepReport
#' @importFrom rtracklayer import
#' @importFrom rtracklayer import.bed
#' @title Final report for single group of regions
#' @description
#' When user call all steps in the pipeline, the final report can be generated.
#' @param prevStep \code{\link{Step-class}} object scalar.
#' Any steps object in this package is acceptable when the pipeline is ready.
#' @param htmlOutput \code{Character} scalar.
#' HTML report file directory
#' Default: NULL ("Report.html")
#' @param createHTML \code{Logical} scalar.
#' If create HTML file. Default: TRUE.
#' This parameter needs to be set FALSE
#' when pandoc or other dependence softwares are not available for rmarkdown package.
#' @param ... Additional arguments, currently unused.
#' @details
#' The report is HTML format. All link in HTML file is the relative directory
#' in report step folder and other step folder
#' If user want to move HTML file and keep all link access available,
#' they should move the whole pipeline folder at the same time.
#' @return An invisible \code{\link{ATACProc-class}}
#' object (\code{\link{Step-class}} based) scalar for downstream analysis.
#' @author Zheng Wei
#' @seealso
#' \code{\link{atacPipe}}
setGeneric("atacSingleRepReport",
function(prevStep, htmlOutput = NULL, createHTML = TRUE,...)
standardGeneric("atacSingleRepReport"))
#' @rdname SingleRepReport
#' @aliases atacSingleRepReport
#' @export
setMethod(
f = "atacSingleRepReport",
signature = "Step",
definition = function(prevStep, htmlOutput = NULL, createHTML = TRUE, ...){
allpara <- c(list(Class = "SingleRepReport",
prevSteps = list(prevStep), isReportStep = TRUE),
as.list(environment()),list(...))
step <- do.call(new,allpara)
invisible(step)
}
)
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