Basic graphic utilities for visualization of genomic data.
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Documentation for package ‘biovizBase’ version 1.46.0
Help Pages
| biovizBase-package | biovizBase is a package which provides utilities and color scheme... |
| addStepping | Adding disjoint levels to a GenomicRanges object |
| addStepping-method | Adding disjoint levels to a GenomicRanges object |
| biovizBase | biovizBase is a package which provides utilities and color scheme... |
| blind.pal.info | Color blind safe palette generator |
| brewer.pal.blind.info | Color blind safe palette generator |
| colorBlindSafePal | Color blind safe palette generator |
| containLetters | Checking if string contains letters or not |
| CRC | CRC |
| crc.gr | CRC |
| crc1.GeRL | crc1.GeRL |
| crunch | Fetching GRanges from various data source |
| crunch-method | Fetching GRanges from various data source |
| darned_hg19_subset500 | Subset of RNA editing sites in hg19... |
| dichromat.pal.blind.info | Color blind safe palette generator |
| estimateCoverage | Estimation of Coverage |
| estimateCoverage-method | Estimation of Coverage |
| flatGrl | Transform GRangesList to GRanges |
| GCcontent | GC content computation for BSgenome |
| genBlindPalInfo | Color blind safe palette generator |
| genBrewerBlindPalInfo | Color blind safe palette generator |
| genDichromatPalInfo | Color blind safe palette generator |
| genesymbol | Gene symbols with position... |
| getBioColor | Color scheme getter for biological data |
| getFormalNames | Get formals from functions |
| getGaps | get gaps for a stepping transformed GRanges object |
| getGaps-method | get gaps for a stepping transformed GRanges object |
| getIdeoGR | Get ideogram information |
| getIdeogram | Get ideogram. |
| getScale | Get scale information from a GRanges |
| getXLab | parse x and y label information from a specific object |
| getXLab-method | parse x and y label information from a specific object |
| getXScale | get x scale breaks and labels |
| getXScale-method | get x scale breaks and labels |
| getYLab | parse x and y label information from a specific object |
| getYLab-method | parse x and y label information from a specific object |
| hg19Ideogram | Hg19 ideogram without cytoband information... |
| hg19IdeogramCyto | Hg19 ideogram with cytoband information... |
| hg19sub | CRC |
| ideo | ideogram without cytoband information |
| ideoCyto | ideogram with cytoband information |
| isIdeogram | Ideogram checking |
| isJunctionRead | Utils for Splicing Summary |
| isMatchedWithModel | Utils for Splicing Summary |
| isSimpleIdeogram | Simple ideogram checking |
| is_coord_genome | Transform GRanges to different coordinates and layout |
| is_coord_truncate_gaps | Shrinkage function |
| maxGap | Estimated max gaps |
| maxGap-method | Estimated max gaps |
| mold | mold data into data.frame |
| mold-method | mold data into data.frame |
| mut.gr | CRC |
| parseArgsForAes | Utils for parsing (un)evaluated arguments |
| parseArgsForNonAes | Utils for parsing (un)evaluated arguments |
| pileupAsGRanges | Summarize reads for certain region |
| pileupGRangesAsVariantTable | Mismatch summary |
| plotColorLegend | Show colors |
| showColor | Show colors |
| shrinkageFun | Shrinkage function |
| shrinkageFun-method | Shrinkage function |
| splitByFacets | split a GRanges by formula |
| splitByFacets-method | split a GRanges by formula |
| strip_formula_dots | strip dots around a formula variables |
| subsetArgsByFormals | Subset list of arguments by functions |
| transformDfToGr | Transform GRanges to different coordinates and layout |
| transformGRangesForEvenSpace | Transform GRanges with New Coordinates |
| transformToArch | Transform GRanges to different coordinates and layout |
| transformToArch-method | Transform GRanges to different coordinates and layout |
| transformToBarInCircle | Transform GRanges to different coordinates and layout |
| transformToCircle | Transform GRanges to different coordinates and layout |
| transformToDf | Transform GRanges to different coordinates and layout |
| transformToDf-method | Transform GRanges to different coordinates and layout |
| transformToGenome | Transform GRanges to different coordinates and layout |
| transformToGenome-method | Transform GRanges to different coordinates and layout |
| transformToLinkInCircle | Transform GRanges to different coordinates and layout |
| transformToRectInCircle | Transform GRanges to different coordinates and layout |
| transformToSegInCircle | Transform GRanges to different coordinates and layout |