upstet print

DESCRIPTION

@@ -4,7 +4,7 @@ Title: Multiple genomic features annotations
 Author: Aurelien Brionne [aut, cre]
 Maintainer: Aurelien Brionne <aurelien.brionne@inra.fr>
 Depends: R (>= 3.6)
-Imports:AnnotationDbi,
+Imports: AnnotationDbi,
         BiocGenerics,
         data.table,
         GenomicFeatures,
@@ -29,7 +29,7 @@ VignetteBuilder: knitr
 License: GPL-3
 URL: https://forgemia.inra.fr/aurelien.brionne/GenomeFeatures
 BugReports: https://forgemia.inra.fr/aurelien.brionne/GenomeFeatures/issues
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0
 Collate: 
     'GFF_att.R'
     'overlapped_genome_features.R'

R/genome_features_overlaps.R

@@ -10,7 +10,7 @@
 #' @importFrom data.table data.table rbindlist .SD .N := melt setorder dcast
 #' @param peaks a  \code{\link[base]{list}} of \code{\link[GenomicRanges]{GRanges}} objects elements provided by \code{\link{readPeakFile}}.
 #' @param features a \code{\link{genome_features-class}} object.
-#' @param figs_path the path where print the \code{\link[UpSetR]{upstet}} plots. ("./data/figs/", by default).
+#' @param figs_path the path where print the \code{\link[UpSetR]{upset}} plots. ("./data/figs/", by default).
 #' @param ignore.strand ignore peak coordinate orientation (defaul to TRUE).
 #' @details This method build a convenient genomic features object, in order to be used for finding overlaps beetween
 #' all needed features and peaks coordinates with \code{\link{genome_features_overlaps}}.
@@ -29,7 +29,7 @@
 #' @exportMethod genome_features_overlaps
 setGeneric(
     name="genome_features_overlaps",
-    def=function(peaks,features,figs_path="./data/figs/",ignore.strand=TRUE){
+    def=function(peaks,features,figs_path=".",ignore.strand=TRUE){
         standardGeneric("genome_features_overlaps")
     }
 )
@@ -371,16 +371,16 @@ setMethod(
 
             # create upset
             png(paste(figs_path,"upset_",x,".png",sep=""))
-                upset(
-                    Data,sets=rev(names(Data)[-1]),
-                    sets.bar.color=rev(colors),
-                    keep.order = TRUE
+                print(
+                    upset(
+                        Data,sets=rev(names(Data)[-1]),
+                        sets.bar.color=rev(colors),
+                        keep.order = TRUE
+                    )
                 )
             dev.off()
         })
 
-        ## create overlapped_genome_features
-
         # createoverlapped_ genome_features
         new(
             "overlapped_genome_features",

man/Plot-methods.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Plot.R
-\docType{methods}
 \name{Plot}
 \alias{Plot}
 \alias{Plot,overlapped_genome_features-method}

man/Table-methods.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Table.R
-\docType{methods}
 \name{Table}
 \alias{Table}
 \alias{Table,overlapped_genome_features-method}

man/build_genome_features-methods.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/build_genome_features.R
-\docType{methods}
 \name{build_genome_features}
 \alias{build_genome_features}
 \alias{build_genome_features,TxDb-method}
 \title{build a convenient genomic features object.}
 \usage{
-build_genome_features(txdb, features = c("promoter", "UTR5", "UTR3",
-  "exon", "intron", "cds", "downstream"),
-  parameters = list(promoter_ranges = list(upstream = 3000, downstream =
-  500), downstream_range = 1000))
+build_genome_features(
+  txdb,
+  features = c("promoter", "UTR5", "UTR3", "exon", "intron", "cds", "downstream"),
+  parameters = list(promoter_ranges = list(upstream = 3000, downstream = 500),
+    downstream_range = 1000)
+)
 
-\S4method{build_genome_features}{TxDb}(txdb, features = c("promoter",
-  "UTR5", "UTR3", "exon", "intron", "cds", "downstream"),
-  parameters = list(promoter_ranges = list(upstream = 3000, downstream =
-  500), downstream_range = 1000))
+\S4method{build_genome_features}{TxDb}(
+  txdb,
+  features = c("promoter", "UTR5", "UTR3", "exon", "intron", "cds", "downstream"),
+  parameters = list(promoter_ranges = list(upstream = 3000, downstream = 500),
+    downstream_range = 1000)
+)
 }
 \arguments{
 \item{txdb}{a txdb database built with \pkg{GenomicFeatures} (see example).}

man/genome_features_overlaps-methods.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/genome_features_overlaps.R
-\docType{methods}
 \name{genome_features_overlaps}
 \alias{genome_features_overlaps}
 \alias{genome_features_overlaps,CompressedGRangesList,genome_features-method}
 \title{find overlaps between genomic coordinates and features.}
 \usage{
-genome_features_overlaps(peaks, features, figs_path = "./data/figs/",
-  ignore.strand = TRUE)
-
+genome_features_overlaps(
+  peaks,
+  features,
+  figs_path = ".",
+  ignore.strand = TRUE
+)
 
-  \S4method{genome_features_overlaps}{CompressedGRangesList,genome_features}(peaks,
-  features, figs_path = "./data/figs/", ignore.strand = TRUE)
+\S4method{genome_features_overlaps}{CompressedGRangesList,genome_features}(
+  peaks,
+  features,
+  figs_path = ".",
+  ignore.strand = TRUE
+)
 }
 \arguments{
 \item{peaks}{a  \code{\link[base]{list}} of \code{\link[GenomicRanges]{GRanges}} objects elements provided by \code{\link{readPeakFile}}.}
 
 \item{features}{a \code{\link{genome_features-class}} object.}
 
-\item{figs_path}{the path where print the \code{\link[UpSetR]{upstet}} plots. ("./data/figs/", by default).}
+\item{figs_path}{the path where print the \code{\link[UpSetR]{upset}} plots. ("./data/figs/", by default).}
 
 \item{ignore.strand}{ignore peak coordinate orientation (defaul to TRUE).}
 }