bioconductor styling package

DESCRIPTION

 Package: GenomeFeatures
 Version: 1.0.0
 Title: Multiple genomic features annotations
-Authors@R: c(
-	person("Aurelien","Brionne", role=c("aut","cre"),
-	email="aurelien.brionne@inra.fr"))
-Depends: R (>= 3.5.2)
-Imports:
-    AnnotationDbi,
-    data.table,
-    GenomicFeatures,
-    GenomicRanges,
-    IRanges,
-    methods,
-    plotly,
-    rtracklayer,
-    UpSetR,
-    BiocStyle,
-    knitr,
-    rmarkdown,
-    remotes,
-    BiocManager
-Description: The aim of this package is to provide a full genomic features annotation from genomic coordinates, without use an annotation priority.
-VignetteBuilder: knitr
-License: GPL-3
-LazyData: TRUE
 Author: Aurelien Brionne [aut, cre]
 Maintainer: Aurelien Brionne <aurelien.brionne@inra.fr>
+Depends: R (>= 3.5)
+Imports:AnnotationDbi,
+        data.table,
+        GenomicFeatures,
+        GenomicRanges,
+        IRanges,
+        methods,
+        plotly,
+        rtracklayer,
+        UpSetR
+Suggests: htmltools,
+          org.Mm.eg.db,
+          Rgraphviz,
+          BiocStyle,
+          knitr,
+          rmarkdown,
+          corrplot,
+          remotes,
+          BiocManager
+Description: The aim of this package is to provide a full genomic features annotation from genomic coordinates, without use an annotation priority.
+VignetteBuilder: knitr
+License: GPL-3 + LICENCE
 URL: https://forgemia.inra.fr/aurelien.brionne/GenomeFeatures
 BugReports: https://forgemia.inra.fr/aurelien.brionne/GenomeFeatures/issues
 RoxygenNote: 6.1.1
@@ -37,5 +36,4 @@ Collate:
     'genome_features.R'
     'build_genome_features.R'
     'genome_features_overlaps.R'
-    'onAttach.R'
     'readPeakFile.R'

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 export(GFF_att)
-export(Plot)
-export(Table)
-export(build_genome_features)
-export(genome_features_overlaps)
 export(readPeakFile)
+exportMethods(Plot)
+exportMethods(Table)
+exportMethods(build_genome_features)
+exportMethods(genome_features_overlaps)
 import(data.table)
-import(rtracklayer)
 importFrom(AnnotationDbi,as.data.frame)
 importFrom(AnnotationDbi,keys)
 importFrom(AnnotationDbi,metadata)
@@ -31,11 +30,15 @@ importFrom(S4Vectors,subjectHits)
 importFrom(UpSetR,upset)
 importFrom(data.table,data.table)
 importFrom(data.table,fread)
+importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,png)
+importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,setClass)
+importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,slot)
 importFrom(methods,slotNames)
 importFrom(plotly,layout)
 importFrom(plotly,plot_ly)
+importFrom(rtracklayer,import)

R/Plot.R

 #' @title  Plot overlapped_genome_features graphs.
 #' @description Plot overlapped_genome_features graphs bar or line.
+#' @importFrom  methods slot setGeneric setMethod
 #' @param object an \code{\link{overlapped_genome_features-class}} object.
 #' @param type a \code{\link[base]{character}} which coulde be "bar" or "line".
 #' @details This method is a simple accessor to the stored \code{\link[plotly]{plot_ly}} bar or line plots from the \code{\link{overlapped_genome_features-class}} object.
@@ -13,15 +14,19 @@
 #' ###################
 #'  # display bar plot
 #' GenomeFeatures::Plot(features_overlaps,"line")
-#' @export
+#' @name Plot
+#' @rdname Plot-methods
+#' @exportMethod Plot
 setGeneric(name="Plot",def=function(object,type){standardGeneric("Plot")})
 
+#' @rdname Plot-methods
+#' @aliases Plot
 setMethod("Plot",signature="overlapped_genome_features",definition=function(object,type) {
 
   ###################
   # display graphs
-  switch(type,
-    bar=object@distribution$bar_plot,
-    line=object@distribution$lines_plot
+  base::switch(type,
+    bar=methods::slot(object,"distribution")$bar_plot,
+    line=methods::slot(object,"distribution")$lines_plot
   )
 })

R/Table.R

 #' @title  extract the annotation table.
 #' @description extract the annotation table from an \code{\link{overlapped_genome_features-class}} object.
+#' @importFrom  methods slot setGeneric setMethod
 #' @param object an \code{\link{overlapped_genome_features-class}} object.
 #' @details This method is a simple accessor to the stored genomic coordinates annnotation \code{\link[data.table]{data.table}}
 #' from an \code{\link{overlapped_genome_features-class}} object.
@@ -9,12 +10,16 @@
 #' ###################
 #  # extract the annotation table
 #' annot<-GenomeFeatures::Table(features_overlaps)
-#' @export
+#' @name Table
+#' @rdname Table-methods
+#' @exportMethod Table
 setGeneric(name="Table",def=function(object){standardGeneric("Table")})
 
+#' @rdname Table-methods
+#' @aliases Table
 setMethod("Table",signature="overlapped_genome_features",definition=function(object){
 
   ###################
   # display the table
-  object@annotation
+  methods::slot(object,"annotation")
 })

R/build_genome_features.R

@@ -55,16 +55,20 @@
 #'    downstream_range=1000
 #'  )
 #' )
-#' @export
+#' @name build_genome_features
+#' @rdname build_genome_features-methods
+#' @exportMethod build_genome_features
 setGeneric(name="build_genome_features",def=function(txdb,features=base::c("promoter","UTR5","UTR3","exon","intron","cds","downstream"),
 parameters=base::list(promoter_ranges=base::list(upstream=3000,downstream=500),downstream_range=1000)){standardGeneric("build_genome_features")})
 
-setMethod("build_genome_features",definition=function(txdb,features,parameters) {
-
-  ###################
-  # check txdb
-  ###################
-  if(base::class(txdb)!="TxDb") base::stop("txdb must be a TxDb class object")
+#' @rdname build_genome_features-methods
+#' @aliases build_genome_features
+setMethod(
+  "build_genome_features",
+  methods::signature(
+    txdb="TxDb"
+  ),
+  definition=function(txdb,features,parameters) {
 
   ###################
   # txdb ids crossref
@@ -83,7 +87,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
   ###################
   # convert TXID to character
-  crossref[,TXID:=base::as.character(TXID)]
+  crossref[,"TXID":=base::as.character(TXID)]
 
   ###################
   # promoters
@@ -103,15 +107,27 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # convert to table
-    promoters_DT<-data.table::data.table(AnnotationDbi::as.data.frame(promoters,row.names = NULL))[,.(tx_id,tx_name)]
+    promoters_DT<-data.table::data.table(
+      AnnotationDbi::as.data.frame(
+        promoters,
+        row.names = NULL
+      )
+    )[,base::c("tx_id","tx_name"),with=FALSE]
 
     ###################
     # convert to character
-    promoters_DT[,tx_id:=base::as.character(tx_id)]
+    promoters_DT[,"tx_id":=base::as.character(promoters_DT$tx_id)]
 
     ###################
     # merge with crossref
-    promoters_DT<-merge(promoters_DT,crossref,by.x="tx_id",by.y="TXID",sort=F,all.x=T)
+    promoters_DT<-merge(
+      promoters_DT,
+      crossref,
+      by.x="tx_id",
+      by.y="TXID",
+      sort=FALSE,
+      all.x=TRUE
+    )
 
     ###################
     # rename
@@ -119,12 +135,17 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # format feature
-    promoters_DT[,  tx_name:=feature]
+    promoters_DT[,"tx_name":=feature]
 
     ###################
     # format feature
     promoters_DT[,`:=`(
-      feature=base::paste(GENEID,feature,"promoter",sep=":"),
+      feature=base::paste(
+        promoters_DT$GENEID,
+        promoters_DT$feature,
+        "promoter",
+        sep=":"
+      ),
       GENEID=NULL,
       TXNAME=NULL
     )]
@@ -141,19 +162,35 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
     ###################
     # get downstream
     downstream<- GenomicFeatures::transcripts(txdb)
-    downstream<-GenomicRanges::flank(downstream,parameters$downstream_range,start=F)
+    downstream<-GenomicRanges::flank(
+      downstream,
+      parameters$downstream_range,
+      start=FALSE
+    )
 
     ###################
     # convert to table
-    downstream_DT<-data.table::data.table(AnnotationDbi::as.data.frame(downstream,,row.names = NULL))[,.(tx_id,tx_name)]
+    downstream_DT<-data.table::data.table(
+      AnnotationDbi::as.data.frame(
+        downstream,
+        row.names = NULL
+      )
+    )[,base::c("tx_id","tx_name"),with=FALSE]
 
     ###################
     # convert to character
-    downstream_DT[,tx_id:=base::as.character(tx_id)]
+    downstream_DT[,"tx_id":=base::as.character(downstream_DT$tx_id)]
 
     ###################
     # merge with crossref
-    downstream_DT<-merge(downstream_DT,crossref,by.x="tx_id",by.y="TXID",sort=F,all.x=T)
+    downstream_DT<-merge(
+      downstream_DT,
+      crossref,
+      by.x="tx_id",
+      by.y="TXID",
+      sort=FALSE,
+      all.x=TRUE
+    )
 
     ###################
     # rename
@@ -161,12 +198,17 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # format feature
-    downstream_DT[,tx_name:=feature]
+    downstream_DT[,"tx_name":=feature]
 
     ###################
     # format feature
     downstream_DT[,`:=`(
-      feature=base::paste(GENEID,feature,"downstream",sep=":"),
+      feature=base::paste(
+        downstream_DT$GENEID,
+        downstream_DT$feature,
+        "downstream",
+        sep=":"
+      ),
       GENEID=NULL,
       TXNAME=NULL
     )]
@@ -182,11 +224,16 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # get 5' UTR in GRangesList
-    UTR5<-GenomicFeatures::fiveUTRsByTranscript(txdb,use.names=F)
+    UTR5<-GenomicFeatures::fiveUTRsByTranscript(txdb,use.names=FALSE)
 
     ###################
     # convert to table
-    UTR5_DT<-data.table::data.table(BiocGenerics::as.data.frame(UTR5,,row.names = NULL))[,.(group_name,exon_rank)]
+    UTR5_DT<-data.table::data.table(
+      BiocGenerics::as.data.frame(
+        UTR5,
+        row.names = NULL
+      )
+    )[,base::c("group_name","exon_rank"),with=FALSE]
 
     ###################
     # convert to GRanges
@@ -194,15 +241,30 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # merge with crossref
-    UTR5_DT<-merge(UTR5_DT,crossref,by.x="group_name",by.y="TXID",sort=F,all.x=T)
+    UTR5_DT<-merge(
+      UTR5_DT,
+      crossref,
+      by.x="group_name",
+      by.y="TXID",
+      sort=FALSE,
+      all.x=TRUE
+    )
 
     ###################
     # format feature
     UTR5_DT[,`:=`(
-      feature=base::paste(GENEID,":",TXNAME,":5'UTR(exon",exon_rank,")",sep=""),
+      feature=base::paste(
+        UTR5_DT$GENEID,
+        ":",
+        UTR5_DT$TXNAME,
+        ":5'UTR(exon",
+        UTR5_DT$exon_rank,
+        ")",
+        sep=""
+      ),
       exon_rank=NULL,
       GENEID=NULL,
-      tx_name=TXNAME,
+      tx_name=UTR5_DT$TXNAME,
       TXNAME=NULL,
       group_name=NULL
     )]
@@ -218,11 +280,16 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # get 3' UTR
-    UTR3<-GenomicFeatures::threeUTRsByTranscript(txdb,use.names=F)
+    UTR3<-GenomicFeatures::threeUTRsByTranscript(txdb,use.names=FALSE)
 
     ###################
     # convert to table
-    UTR3_DT<-data.table::data.table(AnnotationDbi::as.data.frame(UTR3,,row.names = NULL))[,.(group_name,exon_rank)]
+    UTR3_DT<-data.table::data.table(
+      AnnotationDbi::as.data.frame(
+        UTR3,
+        row.names = NULL
+      )
+    )[,base::c("group_name","exon_rank"),with=FALSE]
 
     ###################
     # convert to GRanges
@@ -230,15 +297,30 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # merge with crossref
-    UTR3_DT<-merge(UTR3_DT,crossref,by.x="group_name",by.y="TXID",sort=F,all.x=T)
+    UTR3_DT<-merge(
+      UTR3_DT,
+      crossref,
+      by.x="group_name",
+      by.y="TXID",
+      sort=FALSE,
+      all.x=TRUE
+    )
 
     ###################
     # format feature
     UTR3_DT[,`:=`(
-      feature=base::paste(GENEID,":",TXNAME,":3'UTR(exon",exon_rank,")",sep=""),
+      feature=base::paste(
+        UTR3_DT$GENEID,
+        ":",
+        UTR3_DT$TXNAME,
+        ":3'UTR(exon",
+        UTR3_DT$exon_rank,
+        ")",
+        sep=""
+      ),
       exon_rank=NULL,
       GENEID=NULL,
-      tx_name=TXNAME,
+      tx_name= UTR3_DT$TXNAME,
       TXNAME=NULL,
       group_name=NULL
     )]
@@ -254,11 +336,16 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # get exons
-    exons<-GenomicFeatures::exonsBy(txdb,use.names=F)
+    exons<-GenomicFeatures::exonsBy(txdb,use.names=FALSE)
 
     ###################
     # convert to table
-    exons_DT<-data.table::data.table(AnnotationDbi::as.data.frame(exons,row.names = NULL))[,.(group_name,exon_rank)]
+    exons_DT<-data.table::data.table(
+      AnnotationDbi::as.data.frame(
+        exons,
+        row.names = NULL
+      )
+    )[,base::c("group_name","exon_rank"),with=FALSE]
 
     ###################
     # convert to GRanges
@@ -266,23 +353,45 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # count exons by transcripts
-    exons_nb<-exons_DT[!base::is.na(group_name),.N,by=group_name]
+    exons_nb<-exons_DT[!base::is.na(group_name),.N,by="group_name"]
 
     ###################
     # merge count to exons_DT
-    exons_DT<-merge(exons_DT,exons_nb,by="group_name",all.x=T,sort=F)
+    exons_DT<-merge(
+      exons_DT,
+      exons_nb,
+      by="group_name",
+      all.x=TRUE,
+      sort=FALSE
+    )
 
     ###################
     # merge with crossref
-    exons_DT<-merge(exons_DT,crossref,by.x="group_name",by.y="TXID",sort=F,all.x=T)
+    exons_DT<-merge(
+      exons_DT,
+      crossref,
+      by.x="group_name",
+      by.y="TXID",
+      sort=FALSE,
+      all.x=TRUE
+    )
 
     ###################
     # format feature
     exons_DT[,`:=`(
-      feature=base::paste(GENEID,":",TXNAME,":exon",exon_rank,"/",N,sep=""),
+      feature=base::paste(
+        exons_DT$GENEID,
+        ":",
+        exons_DT$TXNAME,
+        ":exon",
+        exons_DT$exon_rank,
+        "/",
+        exons_DT$N,
+        sep=""
+      ),
       exon_rank=NULL,
       GENEID=NULL,
-      tx_name=TXNAME,
+      tx_name= exons_DT$TXNAME,
       TXNAME=NULL,
       N=NULL,
       group_name=NULL
@@ -299,11 +408,16 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # get introns
-    introns<-GenomicFeatures::intronsByTranscript(txdb,use.names=F)
+    introns<-GenomicFeatures::intronsByTranscript(txdb,use.names=FALSE)
 
     ###################
     # convert to table
-    introns_DT<-data.table::data.table(AnnotationDbi::as.data.frame(introns,row.names = NULL))[,.(group_name,strand)]
+    introns_DT<-data.table::data.table(
+      AnnotationDbi::as.data.frame(
+        introns,
+        row.names = NULL
+      )
+    )[,base::c("group_name","strand"),with=FALSE]
 
     ###################
     # convert to GRanges
@@ -311,32 +425,54 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # count introns by transcripts
-    introns_nb<-introns_DT[!base::is.na(group_name),.N,by=group_name]
+    introns_nb<-introns_DT[!base::is.na(group_name),.N,by="group_name"]
 
     ###################
     # merge count to introns_DT
-    introns_DT<-merge(introns_DT,introns_nb,by="group_name",all.x=T,sort=F)
+    introns_DT<-merge(
+      introns_DT,
+      introns_nb,
+      by="group_name",
+      all.x=TRUE,
+      sort=FALSE
+    )
 
     ###################
     # add intron_rank
-    introns_DT[,intron_rank:=1:base::length(N),by=group_name]
+    introns_DT[,"intron_rank":=1:base::length(N),by="group_name"]
 
     ###################
     # reverse intron_rank for reverse strand
-    introns_DT[strand=="-",intron_rank:=base::rev(intron_rank),by=group_name]
+    introns_DT["-","intron_rank":=base::rev(intron_rank),by="group_name",on="strand"]
 
     ###################
     # merge with crossref
-    introns_DT<-merge(introns_DT,crossref,by.x="group_name",by.y="TXID",sort=F,all.x=T)
+    introns_DT<-merge(
+      introns_DT,
+      crossref,
+      by.x="group_name",
+      by.y="TXID",
+      sort=FALSE,
+      all.x=TRUE
+    )
 
     ###################
     # format feature
     introns_DT[,`:=`(
-      feature=base::paste(GENEID,":",TXNAME,":intron",intron_rank,"/",N,sep=""),
+      feature=base::paste(
+        introns_DT$GENEID,
+        ":",
+        introns_DT$TXNAME,
+        ":intron",
+        introns_DT$intron_rank,
+        "/",
+        introns_DT$N,
+        sep=""
+      ),
       intron_rank=NULL,
       strand=NULL,
       GENEID=NULL,
-      tx_name=TXNAME,
+      tx_name=introns_DT$TXNAME,
       TXNAME=NULL,
       N=NULL,
       group_name=NULL
@@ -353,11 +489,16 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # get exons
-    cds<-GenomicFeatures::cdsBy(txdb,use.names=F)
+    cds<-GenomicFeatures::cdsBy(txdb,use.names=FALSE)
 
     ###################
     # convert to table
-    cds_DT<-data.table::data.table(AnnotationDbi::as.data.frame(cds,row.names = NULL))[,.(group_name,exon_rank)]
+    cds_DT<-data.table::data.table(
+      AnnotationDbi::as.data.frame(
+        cds,
+        row.names = NULL
+      )
+    )[,base::c("group_name","exon_rank"),with=FALSE]
 
     ###################
     # convert to GRanges
@@ -365,23 +506,45 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # count exons by transcripts
-    cds_nb<-cds_DT[!base::is.na(group_name),.N,by=group_name]
+    cds_nb<-cds_DT[!base::is.na(group_name),.N,by="group_name"]
 
     ###################
     # merge count to exons_DT
-    cds_DT<-merge(cds_DT,cds_nb,by="group_name",all.x=T,sort=F)
+    cds_DT<-merge(
+      cds_DT,
+      cds_nb,
+      by="group_name",
+      all.x=TRUE,
+      sort=FALSE
+    )
 
     ###################
     # merge with crossref
-    cds_DT<-merge(cds_DT,crossref,by.x="group_name",by.y="TXID",sort=F,all.x=T)
+    cds_DT<-merge(
+      cds_DT,
+      crossref,
+      by.x="group_name",
+      by.y="TXID",
+      sort=FALSE,
+      all.x=TRUE
+    )
 
     ###################
     # format feature
     cds_DT[,`:=`(
-      feature=base::paste(GENEID,":",TXNAME,":exon",exon_rank,"/",N,sep=""),
+      feature=base::paste(
+        cds_DT$GENEID,
+        ":",
+        cds_DT$TXNAME,
+        ":exon",
+        cds_DT$exon_rank,
+        "/",
+        cds_DT$N,
+        sep=""
+      ),
       exon_rank=NULL,
       GENEID=NULL,
-      tx_name=TXNAME,
+      tx_name=cds_DT$TXNAME,
       TXNAME=NULL,
       N=NULL,
       group_name=NULL
@@ -408,7 +571,11 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
         ###################
         # import the GFF
-        utils::download.file(file,quiet=T,destfile=output)
+        utils::download.file(
+          file,
+