1. Gviz
  2. NAMESPACE
Browse code

Fixed documentation. Version bumped.

Robert Ivánek authored on 17/02/2023 18:33:21
Showing 1 changed files
NAMESPACE
History View file @ a2d5d1e
... ... 
@@ -1,5 +1,6 @@
1 1 
 # Generated by roxygen2: do not edit by hand
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3 
+export(.DisplayPars)
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 export(.chrName)
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 export(.doCache)
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 export(AlignmentsTrack)
Browse code

Restructured the code, split according to the class, first version of roxygen2 documentation. Bumped the version.

Robert Ivánek authored on 21/01/2022 15:52:54
Showing 1 changed files
NAMESPACE
History View file @ 812e4d0
... ... 
@@ -1,194 +1,254 @@
1 
-import(methods)
2 
-
1 
+# Generated by roxygen2: do not edit by hand
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+
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+export(.chrName)
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+export(.doCache)
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+export(AlignmentsTrack)
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+export(AnnotationTrack)
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+export(BiomartGeneRegionTrack)
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+export(CustomTrack)
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+export(DataTrack)
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+export(DetailsAnnotationTrack)
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+export(DisplayPars)
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+export(GeneRegionTrack)
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+export(GenomeAxisTrack)
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+export(HighlightTrack)
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+export(IdeogramTrack)
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+export(OverlayTrack)
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+export(RNASequenceTrack)
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+export(SequenceTrack)
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+export(UcscTrack)
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+export(addScheme)
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+export(availableDefaultMapping)
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+export(availableDisplayPars)
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+export(clearSessionCache)
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+export(drawAxis)
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+export(drawGD)
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+export(exportTracks)
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+export(getScheme)
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+export(plotTracks)
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+exportClasses(AlignmentsTrack)
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+exportClasses(AnnotationTrack)
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+exportClasses(BiomartGeneRegionTrack)
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+exportClasses(CustomTrack)
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+exportClasses(DataTrack)
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+exportClasses(DetailsAnnotationTrack)
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+exportClasses(DisplayPars)
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+exportClasses(GdObject)
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+exportClasses(GeneRegionTrack)
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+exportClasses(GenomeAxisTrack)
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+exportClasses(HighlightTrack)
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+exportClasses(IdeogramTrack)
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+exportClasses(ImageMap)
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+exportClasses(NumericTrack)
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+exportClasses(OverlayTrack)
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+exportClasses(RangeTrack)
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+exportClasses(ReferenceAlignmentsTrack)
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+exportClasses(ReferenceAnnotationTrack)
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+exportClasses(ReferenceDataTrack)
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+exportClasses(ReferenceGeneRegionTrack)
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+exportClasses(ReferenceSequenceTrack)
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+exportClasses(ReferenceTrack)
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+exportClasses(SequenceBSgenomeTrack)
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+exportClasses(SequenceDNAStringSetTrack)
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+exportClasses(SequenceRNAStringSetTrack)
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+exportClasses(SequenceTrack)
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+exportClasses(StackedTrack)
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+exportMethods("[")
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+exportMethods("chromosome<-")
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+exportMethods("displayPars<-")
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+exportMethods("end<-")
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+exportMethods("exon<-")
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+exportMethods("feature<-")
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+exportMethods("gene<-")
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+exportMethods("genome<-")
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+exportMethods("group<-")
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+exportMethods("identifier<-")
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+exportMethods("imageMap<-")
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+exportMethods("stacking<-")
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+exportMethods("start<-")
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+exportMethods("strand<-")
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+exportMethods("symbol<-")
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+exportMethods("transcript<-")
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+exportMethods("values<-")
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+exportMethods("width<-")
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+exportMethods(as.list)
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+exportMethods(chromosome)
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+exportMethods(consolidateTrack)
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+exportMethods(coords)
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+exportMethods(displayPars)
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+exportMethods(drawAxis)
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+exportMethods(drawGD)
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+exportMethods(end)
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+exportMethods(exon)
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+exportMethods(feature)
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+exportMethods(gene)
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+exportMethods(genome)
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+exportMethods(getPar)
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+exportMethods(group)
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+exportMethods(identifier)
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+exportMethods(imageMap)
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+exportMethods(initialize)
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+exportMethods(length)
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+exportMethods(max)
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+exportMethods(min)
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+exportMethods(position)
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+exportMethods(range)
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+exportMethods(seqinfo)
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+exportMethods(seqlevels)
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+exportMethods(seqnames)
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+exportMethods(setCoverage)
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+exportMethods(setPar)
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+exportMethods(setStacks)
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+exportMethods(show)
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+exportMethods(split)
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+exportMethods(stacking)
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+exportMethods(stacks)
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+exportMethods(start)
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+exportMethods(strand)
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+exportMethods(subset)
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+exportMethods(symbol)
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+exportMethods(tags)
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+exportMethods(transcript)
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+exportMethods(values)
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+exportMethods(width)
3 114 
 import(BiocGenerics)
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-import(S4Vectors)
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-import(IRanges)
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-import(XVector)
7 115 
 import(GenomeInfoDb)
8 116 
 import(GenomicRanges)
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+import(IRanges)
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+import(S4Vectors)
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+import(XVector)
9 120 
 import(grid)
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-
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-importClassesFrom(biomaRt, Mart)
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-
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-importClassesFrom(Biostrings, DNAStringSet, RNAStringSet, BStringSet, DNAString, RNAString, BString)
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-
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-importClassesFrom(BSgenome, BSgenome, MaskedBSgenome)
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-
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-importClassesFrom(GenomicFeatures, "TxDb")
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-
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-importClassesFrom(ensembldb, "EnsDb")
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-
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-importClassesFrom(rtracklayer, UCSCData)
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-
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-importMethodsFrom(AnnotationDbi, colnames, get, ls, mget, tail)
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-
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-
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-importMethodsFrom(BSgenome, providerVersion, seqnames)
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-
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-importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", cdsBy, exonsBy, fiveUTRsByTranscript, threeUTRsByTranscript, transcriptsBy, transcripts)
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-
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-importMethodsFrom(ensembldb, cdsBy, exonsBy, fiveUTRsByTranscript, threeUTRsByTranscript, transcriptsBy, transcripts)
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-
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-importMethodsFrom(rtracklayer, chrom, close, getTable, "tableName<-", track,
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-                  ucscTableQuery, trackNames, tableNames, import, import.gff,
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-                  import.gff1, import.gff2, import.gff3, import.2bit, import.bed15,
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-                  import.bw, import.ucsc, import.bed, import.bedGraph, import.chain,
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-                  import.wig, seqinfo)
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-
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-importMethodsFrom(Biostrings, seqtype, "seqtype<-", consensusMatrix, consensusString, unmasked, complement)
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-
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-
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-importFrom(Biobase, listLen, rowMax, rowMin)
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-
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-importFrom(Biostrings, DNAStringSet, RNAStringSet, BStringSet, DNAString, RNAString, BString, reverseComplement, readDNAStringSet, DNA_ALPHABET, stackStrings)
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-
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-importFrom(BSgenome, bsapply)
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-
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-importFrom(biomaRt, getBM, useEnsembl, useMart, listDatasets, listAttributes, listFilters)
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-
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-importFrom(Rsamtools, scanBamFlag, scanBamHeader, scanBam, ScanBamParam, scanFaIndex, scanFa, BamFile, scanBamWhat, bamWhich)
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-
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-importFrom(graphics, par)
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-
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-importFrom(digest, digest)
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-
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-importFrom(grDevices, boxplot.stats, col2rgb, colorRampPalette, extendrange,
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-           hsv, rgb2hsv)
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-
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-importFrom(lattice, current.panel.limits, panel.abline, panel.grid, panel.lines,
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-           panel.points, panel.polygon, panel.segments, panel.xyplot, panel.text,
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-           trellis.par.get)
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-
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-importFrom(matrixStats, colMaxs, rowMedians, rowMins)
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-
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-importFrom(latticeExtra, panel.xyarea, panel.horizonplot)
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-
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-
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-importFrom(RColorBrewer, brewer.pal)
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-
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-importFrom(rtracklayer, GenomicData, ucscGenomes, browserSession, BigWigFile, FastaFile, TwoBitFile)
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-
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-importFrom(stats, loess.smooth)
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-
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-importFrom(biovizBase, getBioColor)
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-
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-importFrom(utils, assignInNamespace, browseURL, write.table)
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-
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-importFrom(GenomicAlignments, extractAlignmentRangesOnReference, cigarRangesAlongReferenceSpace, sequenceLayer, GAlignments, summarizeJunctions)
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-
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-importFrom(grDevices, "dev.cur", "dev.off")
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-
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-importFrom(stats, "setNames")
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-
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-importFrom(utils, "modifyList", "type.convert")
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-
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-###
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-
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-export(".chrName",
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-       ".doCache",
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-       "AlignmentsTrack",
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-       "AnnotationTrack",
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-       "DetailsAnnotationTrack",
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-       "BiomartGeneRegionTrack",
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-       "CustomTrack",
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-       "DataTrack",
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-       "DisplayPars",
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-       "SequenceTrack",
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-       "RNASequenceTrack",
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-       "OverlayTrack",
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-       "drawAxis",
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-       "drawGD",
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-       "GeneRegionTrack",
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-       "GenomeAxisTrack",
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-       "HighlightTrack",
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-       "IdeogramTrack",
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-       "UcscTrack",
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-       "addScheme",
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-       "as.list",
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-       "availableDefaultMapping",
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-       "availableDisplayPars",
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-       "clearSessionCache",
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-       "exportTracks",
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-       "getScheme",
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-       "plotTracks")
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-
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-exportClasses("AlignmentsTrack",
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-              "AnnotationTrack",
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-              "DetailsAnnotationTrack",
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-              "BiomartGeneRegionTrack",
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-              "DataTrack",
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-              "DisplayPars",
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-              "GdObject",
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-              "GeneRegionTrack",
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-              "GenomeAxisTrack",
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-              "IdeogramTrack",
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-              "ImageMap",
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-              "NumericTrack",
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-              "RangeTrack",
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-              "SequenceTrack",
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-              "StackedTrack",
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-              "HighlightTrack",
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-              "OverlayTrack",
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-              "CustomTrack")
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-
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-exportMethods("[",
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-              "as.list",
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-              "chromosome",
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-              "chromosome<-",
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-              "coerce",
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-              "consolidateTrack",
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-              "coords",
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-              "coverage",
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-              "displayPars",
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-              "displayPars<-",
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-              "end",
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-              "end<-",
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-              "exon",
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-              "exon<-",
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-              "feature",
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-              "feature<-",
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-              "gene",
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-              "gene<-",
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-              "genome",
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-              "genome<-",
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-              "getPar",
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-              "group",
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-              "group<-",
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-              "head",
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-              "identifier",
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-              "identifier<-",
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-              "imageMap",
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-              "initialize",
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-              "length",
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-              "max",
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-              "min",
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-              "names",
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-              "names<-",
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-              "position",
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-              "range",
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-              "ranges",
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-              "score",
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-              "seqnames",
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-              "seqlevels",
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-              "seqinfo",
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-              "setPar",
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-              "split",
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-              "stacking",
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-              "stacking<-",
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-              "stacks",
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-              "start",
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-              "start<-",
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-              "strand",
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-              "strand<-",
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-              "subseq",
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-              "subset",
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-              "symbol",
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-              "symbol<-",
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-              "tags",
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-              "tail",
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-              "transcript",
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-              "transcript<-",
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-              "values",
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-              "values<-",
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-              "width",
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-              "width<-")
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+import(methods)
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+importClassesFrom(BSgenome,BSgenome)
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+importClassesFrom(BSgenome,MaskedBSgenome)
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+importClassesFrom(Biostrings,BString)
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+importClassesFrom(Biostrings,BStringSet)
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+importClassesFrom(Biostrings,DNAString)
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+importClassesFrom(Biostrings,DNAStringSet)
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+importClassesFrom(Biostrings,RNAString)
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+importClassesFrom(Biostrings,RNAStringSet)
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+importClassesFrom(GenomicFeatures,TxDb)
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+importClassesFrom(biomaRt,Mart)
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+importClassesFrom(ensembldb,EnsDb)
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+importClassesFrom(rtracklayer,UCSCData)
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+importFrom(BSgenome,bsapply)
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+importFrom(Biobase,listLen)
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+importFrom(Biobase,rowMax)
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+importFrom(Biobase,rowMin)
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+importFrom(Biostrings,BString)
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+importFrom(Biostrings,BStringSet)
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+importFrom(Biostrings,DNAString)
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+importFrom(Biostrings,DNAStringSet)
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+importFrom(Biostrings,DNA_ALPHABET)
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+importFrom(Biostrings,RNAString)
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+importFrom(Biostrings,RNAStringSet)
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+importFrom(Biostrings,readDNAStringSet)
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+importFrom(Biostrings,reverseComplement)
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+importFrom(Biostrings,stackStrings)
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+importFrom(GenomicAlignments,GAlignments)
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+importFrom(GenomicAlignments,cigarRangesAlongReferenceSpace)
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+importFrom(GenomicAlignments,extractAlignmentRangesOnReference)
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+importFrom(GenomicAlignments,sequenceLayer)
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+importFrom(GenomicAlignments,summarizeJunctions)
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+importFrom(RColorBrewer,brewer.pal)
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+importFrom(Rsamtools,BamFile)
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+importFrom(Rsamtools,ScanBamParam)
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+importFrom(Rsamtools,bamWhich)
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+importFrom(Rsamtools,scanBam)
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+importFrom(Rsamtools,scanBamFlag)
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+importFrom(Rsamtools,scanBamHeader)
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+importFrom(Rsamtools,scanBamWhat)
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+importFrom(Rsamtools,scanFa)
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+importFrom(Rsamtools,scanFaIndex)
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+importFrom(biomaRt,getBM)
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+importFrom(biomaRt,listAttributes)
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+importFrom(biomaRt,listDatasets)
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+importFrom(biomaRt,listFilters)
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+importFrom(biomaRt,useEnsembl)
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+importFrom(biomaRt,useMart)
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+importFrom(biovizBase,getBioColor)
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+importFrom(digest,digest)
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+importFrom(grDevices,boxplot.stats)
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+importFrom(grDevices,col2rgb)
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+importFrom(grDevices,colorRampPalette)
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+importFrom(grDevices,dev.cur)
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+importFrom(grDevices,dev.off)
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+importFrom(grDevices,extendrange)
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+importFrom(grDevices,hsv)
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+importFrom(grDevices,rgb2hsv)
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+importFrom(graphics,par)
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+importFrom(lattice,current.panel.limits)
181 
+importFrom(lattice,panel.abline)
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+importFrom(lattice,panel.grid)
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+importFrom(lattice,panel.lines)
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+importFrom(lattice,panel.points)
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+importFrom(lattice,panel.polygon)
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+importFrom(lattice,panel.segments)
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+importFrom(lattice,panel.text)
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+importFrom(lattice,panel.xyplot)
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+importFrom(lattice,trellis.par.get)
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+importFrom(latticeExtra,panel.horizonplot)
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+importFrom(matrixStats,colMaxs)
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+importFrom(matrixStats,rowMedians)
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+importFrom(matrixStats,rowMins)
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+importFrom(rtracklayer,BigWigFile)
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+importFrom(rtracklayer,FastaFile)
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+importFrom(rtracklayer,GenomicData)
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+importFrom(rtracklayer,TwoBitFile)
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+importFrom(rtracklayer,browserSession)
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+importFrom(rtracklayer,ucscGenomes)
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+importFrom(stats,loess.smooth)
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+importFrom(stats,setNames)
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+importFrom(utils,assignInNamespace)
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+importFrom(utils,modifyList)
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+importFrom(utils,type.convert)
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+importFrom(utils,write.table)
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+importMethodsFrom(AnnotationDbi,colnames)
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+importMethodsFrom(AnnotationDbi,get)
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+importMethodsFrom(AnnotationDbi,ls)
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+importMethodsFrom(AnnotationDbi,mget)
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+importMethodsFrom(AnnotationDbi,tail)
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+importMethodsFrom(BSgenome,providerVersion)
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+importMethodsFrom(BSgenome,seqnames)
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+importMethodsFrom(Biostrings,"seqtype<-")
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+importMethodsFrom(Biostrings,complement)
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+importMethodsFrom(Biostrings,consensusMatrix)
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+importMethodsFrom(Biostrings,consensusString)
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+importMethodsFrom(Biostrings,seqtype)
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+importMethodsFrom(Biostrings,unmasked)
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+importMethodsFrom(GenomicFeatures,"isActiveSeq<-")
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+importMethodsFrom(GenomicFeatures,cdsBy)
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+importMethodsFrom(GenomicFeatures,exonsBy)
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+importMethodsFrom(GenomicFeatures,fiveUTRsByTranscript)
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+importMethodsFrom(GenomicFeatures,isActiveSeq)
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+importMethodsFrom(GenomicFeatures,threeUTRsByTranscript)
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+importMethodsFrom(GenomicFeatures,transcripts)
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+importMethodsFrom(GenomicFeatures,transcriptsBy)
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+importMethodsFrom(ensembldb,cdsBy)
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+importMethodsFrom(ensembldb,exonsBy)
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+importMethodsFrom(ensembldb,fiveUTRsByTranscript)
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+importMethodsFrom(ensembldb,threeUTRsByTranscript)
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+importMethodsFrom(ensembldb,transcripts)
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+importMethodsFrom(ensembldb,transcriptsBy)
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+importMethodsFrom(rtracklayer,"tableName<-")
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+importMethodsFrom(rtracklayer,chrom)
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+importMethodsFrom(rtracklayer,close)
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+importMethodsFrom(rtracklayer,getTable)
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+importMethodsFrom(rtracklayer,import)
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+importMethodsFrom(rtracklayer,import.2bit)
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+importMethodsFrom(rtracklayer,import.bed)
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+importMethodsFrom(rtracklayer,import.bed15)
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+importMethodsFrom(rtracklayer,import.bedGraph)
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+importMethodsFrom(rtracklayer,import.bw)
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+importMethodsFrom(rtracklayer,import.chain)
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+importMethodsFrom(rtracklayer,import.gff)
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+importMethodsFrom(rtracklayer,import.gff1)
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+importMethodsFrom(rtracklayer,import.gff2)
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+importMethodsFrom(rtracklayer,import.gff3)
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+importMethodsFrom(rtracklayer,import.ucsc)
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+importMethodsFrom(rtracklayer,import.wig)
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+importMethodsFrom(rtracklayer,seqinfo)
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+importMethodsFrom(rtracklayer,tableNames)
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+importMethodsFrom(rtracklayer,track)
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+importMethodsFrom(rtracklayer,trackNames)
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+importMethodsFrom(rtracklayer,ucscTableQuery)
Browse code

Remove AlignedReadTrack functions.

Robert Ivánek authored on 06/01/2022 15:39:34
Showing 1 changed files
NAMESPACE
History View file @ 78bbfbc
... ... 
@@ -86,7 +86,6 @@ importFrom(utils, "modifyList", "type.convert")
86 86
87 87 
 export(".chrName",
88 88 
        ".doCache",
89 
-       "AlignedReadTrack",
90 89 
        "AlignmentsTrack",
91 90 
        "AnnotationTrack",
92 91 
        "DetailsAnnotationTrack",
Browse code

Switched to useEnsembl istead of useMart

Robert Ivánek authored on 06/01/2022 15:09:36
Showing 1 changed files
NAMESPACE
History View file @ a6b04ea
... ... 
@@ -44,7 +44,7 @@ importFrom(Biostrings, DNAStringSet, RNAStringSet, BStringSet, DNAString, RNAStr
44 44
45 45 
 importFrom(BSgenome, bsapply)
46 46
47 
-importFrom(biomaRt, getBM, useMart, listDatasets, listAttributes, listFilters)
47 
+importFrom(biomaRt, getBM, useEnsembl, useMart, listDatasets, listAttributes, listFilters)
48 48
49 49 
 importFrom(Rsamtools, scanBamFlag, scanBamHeader, scanBam, ScanBamParam, scanFaIndex, scanFa, BamFile, scanBamWhat, bamWhich)
50 50
Browse code

Clean-up after defunct

Robert Ivánek authored on 23/11/2020 10:25:39
Showing 1 changed files
NAMESPACE
History View file @ bfe10e3
... ... 
@@ -113,8 +113,7 @@ export(".chrName",
113 113 
        "getScheme",
114 114 
        "plotTracks")
115 115
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-exportClasses("AlignedReadTrack",
117 
-              "AlignmentsTrack",
116 
+exportClasses("AlignmentsTrack",
118 117 
               "AnnotationTrack",
119 118 
               "DetailsAnnotationTrack",
120 119 
               "BiomartGeneRegionTrack",
Browse code

added possibility to create GeneRegionTrack from EnsDb

Robert Ivánek authored on 05/03/2020 13:35:36
Showing 1 changed files
NAMESPACE
History View file @ d43138a
... ... 
@@ -16,6 +16,8 @@ importClassesFrom(BSgenome, BSgenome, MaskedBSgenome)
16 16
17 17 
 importClassesFrom(GenomicFeatures, "TxDb")
18 18
19 
+importClassesFrom(ensembldb, "EnsDb")
20 
+
19 21 
 importClassesFrom(rtracklayer, UCSCData)
20 22
21 23 
 importMethodsFrom(AnnotationDbi, colnames, get, ls, mget, tail)
... ... 
@@ -25,6 +27,8 @@ importMethodsFrom(BSgenome, providerVersion, seqnames)
25 27
26 28 
 importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", cdsBy, exonsBy, fiveUTRsByTranscript, threeUTRsByTranscript, transcriptsBy, transcripts)
27 29
30 
+importMethodsFrom(ensembldb, cdsBy, exonsBy, fiveUTRsByTranscript, threeUTRsByTranscript, transcriptsBy, transcripts)
31 
+
28 32 
 importMethodsFrom(rtracklayer, chrom, close, getTable, "tableName<-", track,
29 33 
                   ucscTableQuery, trackNames, tableNames, import, import.gff,
30 34 
                   import.gff1, import.gff2, import.gff3, import.2bit, import.bed15,
Browse code

Clenaup of code (tab to 4spaces)

Robert Ivánek authored on 19/02/2020 20:27:14
Showing 1 changed files
NAMESPACE
History View file @ f9136dd
... ... 
@@ -116,15 +116,15 @@ exportClasses("AlignedReadTrack",
116 116 
               "BiomartGeneRegionTrack",
117 117 
               "DataTrack",
118 118 
               "DisplayPars",
119 
-	      "GdObject",
119 
+              "GdObject",
120 120 
               "GeneRegionTrack",
121 121 
               "GenomeAxisTrack",
122 122 
               "IdeogramTrack",
123 123 
               "ImageMap",
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-	      "NumericTrack",
125 
-	      "RangeTrack",
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+              "NumericTrack",
125 
+              "RangeTrack",
126 126 
               "SequenceTrack",
127 
-	      "StackedTrack",
127 
+              "StackedTrack",
128 128 
               "HighlightTrack",
129 129 
               "OverlayTrack",
130 130 
               "CustomTrack")
Browse code

fixed issues in man pages

Robert Ivánek authored on 13/02/2020 20:38:16
Showing 1 changed files
NAMESPACE
History View file @ 8b94421
... ... 
@@ -21,7 +21,7 @@ importClassesFrom(rtracklayer, UCSCData)
21 21 
 importMethodsFrom(AnnotationDbi, colnames, get, ls, mget, tail)
22 22
23 23
24 
-importMethodsFrom(BSgenome, providerVersion)
24 
+importMethodsFrom(BSgenome, providerVersion, seqnames)
25 25
26 26 
 importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", cdsBy, exonsBy, fiveUTRsByTranscript, threeUTRsByTranscript, transcriptsBy, transcripts)
27 27
... ... 
@@ -91,6 +91,7 @@ export(".chrName",
91 91 
        "DataTrack",
92 92 
        "DisplayPars",
93 93 
        "SequenceTrack",
94 
+       "RNASequenceTrack",
94 95 
        "OverlayTrack",
95 96 
        "drawAxis",
96 97 
        "drawGD",
Browse code

Added missing entries in man and NAMESPACE

Robert Ivánek authored on 13/02/2020 19:14:49
Showing 1 changed files
NAMESPACE
History View file @ 2085cae
... ... 
@@ -38,6 +38,8 @@ importFrom(Biobase, listLen, rowMax, rowMin)
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 importFrom(Biostrings, DNAStringSet, RNAStringSet, BStringSet, DNAString, RNAString, BString, reverseComplement, readDNAStringSet, DNA_ALPHABET, stackStrings)
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+importFrom(BSgenome, bsapply)
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+
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 importFrom(biomaRt, getBM, useMart, listDatasets, listAttributes, listFilters)
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 importFrom(Rsamtools, scanBamFlag, scanBamHeader, scanBam, ScanBamParam, scanFaIndex, scanFa, BamFile, scanBamWhat, bamWhich)
Browse code

Added the possibility to visualize the indels in the AlignmentsTrack. Bumped version.

Robert Ivánek authored on 12/02/2020 16:02:35
Showing 1 changed files
NAMESPACE
History View file @ 4a7e3e4
... ... 
@@ -68,7 +68,7 @@ importFrom(biovizBase, getBioColor)
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 importFrom(utils, assignInNamespace, browseURL, write.table)
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-importFrom(GenomicAlignments, extractAlignmentRangesOnReference, sequenceLayer, GAlignments, summarizeJunctions)
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+importFrom(GenomicAlignments, extractAlignmentRangesOnReference, cigarRangesAlongReferenceSpace, sequenceLayer, GAlignments, summarizeJunctions)
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 importFrom(grDevices, "dev.cur", "dev.off")
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Browse code

fixed wrong setter import in NAMESPACE

Felix Ernst authored on 05/10/2019 06:59:09 • GitHub committed on 05/10/2019 06:59:09
Showing 1 changed files
NAMESPACE
History View file @ 6856636
... ... 
@@ -31,7 +31,7 @@ importMethodsFrom(rtracklayer, chrom, close, getTable, "tableName<-", track,
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                   import.bw, import.ucsc, import.bed, import.bedGraph, import.chain,
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                   import.wig, seqinfo)
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-importMethodsFrom(Biostrings, seqtype, seqtype<-, consensusMatrix, consensusString, unmasked, complement)
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+importMethodsFrom(Biostrings, seqtype, "seqtype<-", consensusMatrix, consensusString, unmasked, complement)
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 importFrom(Biobase, listLen, rowMax, rowMin)
Browse code

Update NAMESPACE

Felix Ernst authored on 04/10/2019 19:37:52
Showing 1 changed files
NAMESPACE
History View file @ 57f78ce
... ... 
@@ -31,7 +31,7 @@ importMethodsFrom(rtracklayer, chrom, close, getTable, "tableName<-", track,
31 31 
                   import.bw, import.ucsc, import.bed, import.bedGraph, import.chain,
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                   import.wig, seqinfo)
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-importMethodsFrom(Biostrings, consensusMatrix, consensusString, unmasked, complement)
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+importMethodsFrom(Biostrings, seqtype, seqtype<-, consensusMatrix, consensusString, unmasked, complement)
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 importFrom(Biobase, listLen, rowMax, rowMin)
Browse code

Added SequenceRNAStringSetTrack class

Refactored some internals to support SequenceTrack object representing other nucleotide sequences

Felix Ernst authored on 03/10/2019 07:12:24
Showing 1 changed files
NAMESPACE
History View file @ a36c930
... ... 
@@ -10,7 +10,7 @@ import(grid)
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 importClassesFrom(biomaRt, Mart)
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-importClassesFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString)
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+importClassesFrom(Biostrings, DNAStringSet, RNAStringSet, BStringSet, DNAString, RNAString, BString)
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 importClassesFrom(BSgenome, BSgenome, MaskedBSgenome)
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@@ -36,7 +36,7 @@ importMethodsFrom(Biostrings, consensusMatrix, consensusString, unmasked, comple
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 importFrom(Biobase, listLen, rowMax, rowMin)
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-importFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString, reverseComplement, readDNAStringSet, DNA_ALPHABET, stackStrings)
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+importFrom(Biostrings, DNAStringSet, RNAStringSet, BStringSet, DNAString, RNAString, BString, reverseComplement, readDNAStringSet, DNA_ALPHABET, stackStrings)
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 importFrom(biomaRt, getBM, useMart, listDatasets, listAttributes, listFilters)
42 42
Browse code

exported drawAxis, fixed some typos, replaced Florian ad a maintainer

Robert Ivánek authored on 15/02/2018 13:58:49
Showing 1 changed files
NAMESPACE
History View file @ 691b67c
... ... 
@@ -23,7 +23,7 @@ importMethodsFrom(AnnotationDbi, colnames, get, ls, mget, tail)
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 importMethodsFrom(BSgenome, providerVersion)
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-importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", exonsBy, transcriptsBy, transcripts)
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+importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", cdsBy, exonsBy, fiveUTRsByTranscript, threeUTRsByTranscript, transcriptsBy, transcripts)
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 importMethodsFrom(rtracklayer, chrom, close, getTable, "tableName<-", track,
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                   ucscTableQuery, trackNames, tableNames, import, import.gff,
... ... 
@@ -90,6 +90,7 @@ export(".chrName",
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        "DisplayPars",
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        "SequenceTrack",
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        "OverlayTrack",
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+       "drawAxis",
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        "drawGD",
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        "GeneRegionTrack",
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        "GenomeAxisTrack",
Browse code

making the Biomart connections to non-standard genomes a bit more robust

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@124735 bc3139a8-67e5-0310-9ffc-ced21a209358

Florian Hahne authored on 02/12/2016 13:04:47
Showing 1 changed files
NAMESPACE
History View file @ 0b8d0ca
... ... 
@@ -70,6 +70,12 @@ importFrom(utils, assignInNamespace, browseURL, write.table)
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 importFrom(GenomicAlignments, extractAlignmentRangesOnReference, sequenceLayer, GAlignments, summarizeJunctions)
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+importFrom(grDevices, "dev.cur", "dev.off")
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+
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+importFrom(stats, "setNames")
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+
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+importFrom(utils, "modifyList", "type.convert")
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+
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 ###
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 export(".chrName",
Browse code

added sashimi plots to the AlignmentsTrack

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@101285 bc3139a8-67e5-0310-9ffc-ced21a209358

Robert Ivanek authored on 27/03/2015 13:20:00
Showing 1 changed files
NAMESPACE
History View file @ 74a120f
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@@ -68,7 +68,7 @@ importFrom(biovizBase, getBioColor)
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 importFrom(utils, assignInNamespace, browseURL, write.table)
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-importFrom(GenomicAlignments, extractAlignmentRangesOnReference, sequenceLayer)
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+importFrom(GenomicAlignments, extractAlignmentRangesOnReference, sequenceLayer, GAlignments, summarizeJunctions)
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 ###
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Browse code

BiomartGeneRegionTracks are now streaming data

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@99132 bc3139a8-67e5-0310-9ffc-ced21a209358

Florian Hahne authored on 06/02/2015 15:51:43
Showing 1 changed files
NAMESPACE
History View file @ bbc4a5c
... ... 
@@ -31,7 +31,7 @@ importMethodsFrom(rtracklayer, chrom, close, getTable, "tableName<-", track,
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                   import.bw, import.ucsc, import.bed, import.bedGraph, import.chain,
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                   import.wig, seqinfo)
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-importMethodsFrom(Biostrings, consensusMatrix)
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+importMethodsFrom(Biostrings, consensusMatrix, consensusString, unmasked, complement)
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 importFrom(Biobase, listLen, rowMax, rowMin)
Browse code

BiomartGeneRegionTracks will now stream new data on demand

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@99075 bc3139a8-67e5-0310-9ffc-ced21a209358

Florian Hahne authored on 05/02/2015 11:10:21
Showing 1 changed files
NAMESPACE
History View file @ b23b2cb
... ... 
@@ -20,7 +20,6 @@ importClassesFrom(rtracklayer, UCSCData)
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 importMethodsFrom(AnnotationDbi, colnames, get, ls, mget, tail)
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-importMethodsFrom(Biobase, rowMedians)
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 importMethodsFrom(BSgenome, providerVersion)
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@@ -39,12 +38,14 @@ importFrom(Biobase, listLen, rowMax, rowMin)
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 importFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString, reverseComplement, readDNAStringSet, DNA_ALPHABET, stackStrings)
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-importFrom(biomaRt, getBM, useMart)
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+importFrom(biomaRt, getBM, useMart, listDatasets, listAttributes, listFilters)
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 importFrom(Rsamtools, scanBamFlag, scanBamHeader, scanBam, ScanBamParam, scanFaIndex, scanFa, BamFile, scanBamWhat, bamWhich)
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 importFrom(graphics, par)
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+importFrom(digest, digest)
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+
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 importFrom(grDevices, boxplot.stats, col2rgb, colorRampPalette, extendrange,
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            hsv, rgb2hsv)
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... ... 
@@ -52,7 +53,7 @@ importFrom(lattice, current.panel.limits, panel.abline, panel.grid, panel.lines,
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            panel.points, panel.polygon, panel.segments, panel.xyplot, panel.text,
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            trellis.par.get)
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-importFrom(matrixStats, colMaxs)
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+importFrom(matrixStats, colMaxs, rowMedians, rowMins)
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 importFrom(latticeExtra, panel.xyarea, panel.horizonplot)
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@@ -69,7 +70,6 @@ importFrom(utils, assignInNamespace, browseURL, write.table)
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 importFrom(GenomicAlignments, extractAlignmentRangesOnReference, sequenceLayer)
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-importFrom(grid)
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 ###
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 export(".chrName",
Browse code

importing the whole grid name space

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@98060 bc3139a8-67e5-0310-9ffc-ced21a209358

Florian Hahne authored on 06/01/2015 13:20:41
Showing 1 changed files
NAMESPACE
History View file @ 219e47a
... ... 
@@ -69,6 +69,7 @@ importFrom(utils, assignInNamespace, browseURL, write.table)
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 importFrom(GenomicAlignments, extractAlignmentRangesOnReference, sequenceLayer)
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+importFrom(grid)
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 ###
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 export(".chrName",
Browse code

adding some code to better deal with ENSEMBL schema changes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@96205 bc3139a8-67e5-0310-9ffc-ced21a209358

Florian Hahne authored on 30/10/2014 11:38:35
Showing 1 changed files
NAMESPACE
History View file @ 16a1192
... ... 
@@ -6,6 +6,7 @@ import(IRanges)
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 import(XVector)
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 import(GenomeInfoDb)
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 import(GenomicRanges)
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+import(grid)
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 importClassesFrom(biomaRt, Mart)
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@@ -47,13 +48,6 @@ importFrom(graphics, par)
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 importFrom(grDevices, boxplot.stats, col2rgb, colorRampPalette, extendrange,
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            hsv, rgb2hsv)
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-importFrom(grid, convertHeight, convertWidth, convertX, convertY,
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-           current.transform, current.viewport, current.vpTree, dataViewport,
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-           downViewport, gpar, grid.circle, grid.lines, grid.newpage,
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-           grid.polygon, grid.rect, grid.segments, grid.text, grid.yaxis,
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-           popViewport, pushViewport, stringHeight, stringWidth, unit,
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-           upViewport, viewport)
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-
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 importFrom(lattice, current.panel.limits, panel.abline, panel.grid, panel.lines,
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            panel.points, panel.polygon, panel.segments, panel.xyplot, panel.text,
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            trellis.par.get)
Browse code

Adding a missing export for the CustomTrack constructor

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@93728 bc3139a8-67e5-0310-9ffc-ced21a209358

Florian Hahne authored on 01/09/2014 09:49:31
Showing 1 changed files
NAMESPACE
History View file @ 0e9a727
... ... 
@@ -84,6 +84,7 @@ export(".chrName",
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        "AnnotationTrack",
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        "DetailsAnnotationTrack",
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        "BiomartGeneRegionTrack",
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+       "CustomTrack",
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        "DataTrack",
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        "DisplayPars",
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        "SequenceTrack",
Browse code

follow renaming of TranscriptDb class -> TxDb

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@92980 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 28/07/2014 23:22:02
Showing 1 changed files
NAMESPACE
History View file @ 4bbe1bb
... ... 
@@ -13,7 +13,7 @@ importClassesFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString)
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 importClassesFrom(BSgenome, BSgenome, MaskedBSgenome)
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-importClassesFrom(GenomicFeatures, "TranscriptDb")
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+importClassesFrom(GenomicFeatures, "TxDb")
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 importClassesFrom(rtracklayer, UCSCData)
19 19
Browse code

follow Rle move from IRanges to S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@92353 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 09/07/2014 23:32:02
Showing 1 changed files
NAMESPACE
History View file @ 7b50ba4
... ... 
@@ -1,5 +1,6 @@
1 1 
 import(methods)
2 2
3 
+import(BiocGenerics)
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 import(S4Vectors)
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 import(IRanges)
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 import(XVector)
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@@ -20,10 +21,6 @@ importMethodsFrom(AnnotationDbi, colnames, get, ls, mget, tail)
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 importMethodsFrom(Biobase, rowMedians)
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-importMethodsFrom(BiocGenerics, cbind, duplicated, eval, intersect, lapply,
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-                  mapply, order, paste, pmax, pmin, rbind, sapply, setdiff,
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-                  table, tapply, unique)
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-
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 importMethodsFrom(BSgenome, providerVersion)
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 importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", exonsBy, transcriptsBy, transcripts)
... ... 
@@ -41,8 +38,6 @@ importFrom(Biobase, listLen, rowMax, rowMin)
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 importFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString, reverseComplement, readDNAStringSet, DNA_ALPHABET, stackStrings)
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-importFrom(BiocGenerics, getObjectSlots)
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-
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 importFrom(biomaRt, getBM, useMart)
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 importFrom(Rsamtools, scanBamFlag, scanBamHeader, scanBam, ScanBamParam, scanFaIndex, scanFa, BamFile, scanBamWhat, bamWhich)
Browse code

adding CustomTracks class

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@90986 bc3139a8-67e5-0310-9ffc-ced21a209358

Florian Hahne authored on 04/06/2014 12:19:57
Showing 1 changed files
NAMESPACE
History View file @ 453554a
... ... 
@@ -125,7 +125,8 @@ exportClasses("AlignedReadTrack",
125 125 
               "SequenceTrack",
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 	      "StackedTrack",
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               "HighlightTrack",
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-              "OverlayTrack")
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+              "OverlayTrack",
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+              "CustomTrack")
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 exportMethods("[",
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               "as.list",
Browse code

resync with latest changes in GenomicRanges/GenomeInfoDb

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@89957 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 06/05/2014 05:15:18
Showing 1 changed files
NAMESPACE
History View file @ 8be2fca
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@@ -3,6 +3,7 @@ import(methods)
3 3 
 import(S4Vectors)
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 import(IRanges)
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 import(XVector)
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+import(GenomeInfoDb)
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 import(GenomicRanges)
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 importClassesFrom(biomaRt, Mart)
Browse code

need to have GenomicRanges in Depends

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@89255 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 19/04/2014 20:04:13
Showing 1 changed files
NAMESPACE
History View file @ f3cad77
... ... 
@@ -1,27 +1,18 @@
1 
-#Generated by codetoolsBioC version 0.0.16
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-#Timestamp: Tue Feb 14 10:11:41 2012
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-
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-#Imports: AnnotationDbi, Biobase, BiocGenerics, biomaRt, GenomicRanges,
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-#         graphics, grDevices, grid, IRanges, lattice, methods, RColorBrewer,
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-#         rtracklayer, stats, utils
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-
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 import(methods)
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+import(S4Vectors)
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+import(IRanges)
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+import(XVector)
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+import(GenomicRanges)
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+
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 importClassesFrom(biomaRt, Mart)
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 importClassesFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString)
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-importClassesFrom(GenomicRanges, GRanges)
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-
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 importClassesFrom(BSgenome, BSgenome, MaskedBSgenome)
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 importClassesFrom(GenomicFeatures, "TranscriptDb")
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-importClassesFrom(IRanges, IRanges, NormalIRanges)
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-
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-importClassesFrom(XVector, GroupedIRanges)
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-
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-
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 importClassesFrom(rtracklayer, UCSCData)
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 importMethodsFrom(AnnotationDbi, colnames, get, ls, mget, tail)
... ... 
@@ -36,21 +27,6 @@ importMethodsFrom(BSgenome, providerVersion)
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 importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", exonsBy, transcriptsBy, transcripts)
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-importMethodsFrom(GenomicRanges, genome, "genome<-", mcols, "mcols<-",
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-                  seqlengths, seqnames, seqlevels, seqinfo, strand, "strand<-",
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-                  seqnameStyle, shift)
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-
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-importMethodsFrom(IRanges, as.data.frame, as.list, as.matrix, as.vector,
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-                  "colnames<-", coverage, diff, disjointBins, end, "end<-", range,
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-                  findOverlaps, findRun, gsub, ifelse, "%in%", levels, match,
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-                  mean, ncol, nrow, queryHits, ranges, "ranges<-", reduce, rev,
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-                  Rle, rownames, "rownames<-", runmean, runValue, "runValue<-",
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-                  score, sort, split, start, "start<-", sub, subjectHits,
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-                  substring, t, tolower, unlist, values, "values<-", which,
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-                  which.max, width, "width<-", endoapply,
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-                  elementLengths, overlapsAny)
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-
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-
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 importMethodsFrom(rtracklayer, chrom, close, getTable, "tableName<-", track,
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                   ucscTableQuery, trackNames, tableNames, import, import.gff,
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                   import.gff1, import.gff2, import.gff3, import.2bit, import.bed15,
... ... 
@@ -68,8 +44,6 @@ importFrom(BiocGenerics, getObjectSlots)
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 importFrom(biomaRt, getBM, useMart)
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-importFrom(GenomicRanges, GRanges, renameSeqlevels)
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-
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 importFrom(Rsamtools, scanBamFlag, scanBamHeader, scanBam, ScanBamParam, scanFaIndex, scanFa, BamFile, scanBamWhat, bamWhich)
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 importFrom(graphics, par)
... ... 
@@ -84,10 +58,6 @@ importFrom(grid, convertHeight, convertWidth, convertX, convertY,
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            popViewport, pushViewport, stringHeight, stringWidth, unit,
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            upViewport, viewport)
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-importFrom(IRanges, IRanges, DataFrame)
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-
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-importFrom(XVector, subseq)
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-
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 importFrom(lattice, current.panel.limits, panel.abline, panel.grid, panel.lines,
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            panel.points, panel.polygon, panel.segments, panel.xyplot, panel.text,
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            trellis.par.get)
... ... 
@@ -105,7 +75,7 @@ importFrom(stats, loess.smooth)
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 importFrom(biovizBase, getBioColor)
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-importFrom(utils, assignInNamespace, browseURL, head, write.table)
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+importFrom(utils, assignInNamespace, browseURL, write.table)
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 importFrom(GenomicAlignments, extractAlignmentRangesOnReference, sequenceLayer)
111 81
Browse code

resync with stuff moving from IRanges to S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@89254 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 19/04/2014 19:49:22
Showing 1 changed files
NAMESPACE
History View file @ a035be8
... ... 
@@ -36,7 +36,7 @@ importMethodsFrom(BSgenome, providerVersion)
36 36
37 37 
 importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", exonsBy, transcriptsBy, transcripts)
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-importMethodsFrom(GenomicRanges, "elementMetadata<-", genome, "genome<-", mcols, "mcols<-",
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+importMethodsFrom(GenomicRanges, genome, "genome<-", mcols, "mcols<-",
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                   seqlengths, seqnames, seqlevels, seqinfo, strand, "strand<-",
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                   seqnameStyle, shift)
42 42
... ... 
@@ -47,7 +47,7 @@ importMethodsFrom(IRanges, as.data.frame, as.list, as.matrix, as.vector,
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                   Rle, rownames, "rownames<-", runmean, runValue, "runValue<-",
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                   score, sort, split, start, "start<-", sub, subjectHits,
49 49 
                   substring, t, tolower, unlist, values, "values<-", which,
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-                  which.max, width, "width<-", elementMetadata, endoapply,
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+                  which.max, width, "width<-", endoapply,
51 51 
                   elementLengths, overlapsAny)
52 52
53 53
... ... 
@@ -166,7 +166,6 @@ exportMethods("[",
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               "coverage",
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               "displayPars",
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               "displayPars<-",
169 
-              "elementMetadata<-",
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               "end",
171 170 
               "end<-",
172 171 
               "exon"