#' Create report of QC
#'
#' @param path absolute path to bcbio results (in yaml file after -upload)
#' @param samples vector indicating the name as samples are in the previous folder
#' @param out path where you want to create the index.html
#' @param title this value would be the title of the document
#' @param condition a vector indicating the groups of the samples
#' @export
#' @examples
#' \dontrun{
#' p<-"absolute paht to bcbio results in yaml file: -upload
#' s<-c("name1","name2","name3","name4")
#' o<-"/path/where/html/will/be/created"
#' t<-"some title for the report"
#' con<-c("TREAT","TREAT","CON","CON")
#' r<-create_report(p,s,o,t,con)
#' }
create_report<-function(path,samples,out,title,condition){
require(Nozzle.R1)
report<-""
report <- newCustomReport( title );
#report <- addTo( report, addTo( newSection( "My Introduction" ),
# newParagraph( "Hello World! This is a paragraph of text!" ) ) );
#report <- addTo( report, addTo( newSection( "My Methods" ),
# method ) );
FRfqc<- i_create_fastqc_figure(path,samples,out)
Trqc<- i_create_mapping_stats(path,samples,out)
FRfrccov<- i_create_gene_coverage(path,samples,out)
Tcounts<- i_create_count_top(path,samples,out)
FRcounts <- i_create_distribution_counts(path,samples,out,condition)
report <- addTo(
report, addTo( newSection( "Quality of samples", class="results" ),
addTo( newSubSection( "Quality of base calling" ), FRfqc),
addTo( newSubSection( "Mapping stats" ), Trqc),
addTo( newSubSection("Gene coverage"), FRfrccov),
addTo( newSubSection( "Top expressed genes" ), Tcounts),
addTo( newSubSection( "Counts distribution" ), FRcounts[[1]]),
addTo( newSubSection( "Normalized counts distribution" ), FRcounts[[2]]),
addTo( newSubSection("Cumulative expression"), FRcounts[[3]]),
addTo( newSubSection( "Samples similarity" ), FRcounts[[4]])
)
);
return(report)
}
#' Write report of QC
#'
#' @param report an object comming from create_report()
#' @param out path where you want to create the index.html (same as used in create_report)
#' @export
#' @examples
#' \dontrun{
#' p<-"absolute path to bcbio results in yaml file: -upload
#' s<-c("name1","name2","name3","name4")
#' o<-"/path/where/html/will/be/created"
#' t<-"some title for the report"
#' con<-c("TREAT","TREAT","CON","CON")
#' r<-write_report(p,s,o,t,con)
#' }
write_report<-function(report,outfile){
writeReport( report, filename=paste(outfile,"/QC.html",sep=""));
}
add_DE<-function(report,defile,condition){
report <- addTo(
report,
addTo(newSection("DE",class="results"),
addTo(newSubSection("DE genes"),Tedger),
addTo(newSubSection("Quality of DE analysis"),FRpval)
)
)
return(report)
}
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