Man pages for daewoooo/SVbyEye
Visualization of genomic structural variants
| addAlignments | Add PAF alignments to a SVbyEye miropeat style plot. |
| addAnnotation | Add annotation ranges to a SVbyEye plot. |
| add.control.points | Function to add bezier control points for horizontal layout. |
| addSelfAlignments | Add PAF self-alignments to a SVbyEye miropeat style plot. |
| breakPaf | A wrapper function for 'breakPafAlignment' expanding multiple... |
| breakPafAlignment | Function to break PAF alignment into matching bases between... |
| cigar2ranges | Function to load CIGAR string reported in PAF alignments into... |
| collapsePaf | Collapse PAF query and target ranges based on unique... |
| disjoinPafAlignments | Disjoin overlapping PAF alignments. |
| fasta2nucleotideContent | Get sequence content from a single FASTA file. |
| filterPaf | Filter PAF alignments. |
| flipPaf | Flip orientation of PAF alignments. |
| flipQueryAnnotation | Flip query annotation ranges |
| geom_arrowhead | A 'ggplot2' geom to draw genomic ranges as arrowheads. |
| geom_miropeats | A 'ggplot2' geom to draw genomic alignments in a miropeats... |
| geom_roundrect | A 'ggplot2' geom to draw genomic ranges as round rectangles. |
| geom_wide_arc | A 'ggplot2' geom to draw arcs between genomic alignments. |
| getAnnotationLevels | Assign each genomic range a non-overlapping level value |
| getColorScheme | Add color scheme based on certain values and defined breaks. |
| getNucleotideContent | Get sequence content from one or multiple FASTA sequences. |
| liftRangesToAlignment | Function to lift coordinates to the alignment in PAF format. |
| maskFASTA | Mask FASTA sequence at defined regions. |
| mirrorRanges | Mirror/reflect genomic ranges given the sequence length. |
| nucmer2PAF | Read nucmer coordinates file in to PAF formatted table |
| paf2continuousScale | Define shift of genomic coordinates in order to get... |
| paf2coords | Prepare PAF alignments for plotting. |
| paf2FASTA | Export FASTA sequences from a set of alignments reported in... |
| paf2gaps | Report gaps between PAF alignments. |
| paf2nucleotideContent | Add FASTA sequence content to PAF alignments. |
| pafAlignmentToBins | Function to break PAF alignment into matching bases between... |
| pafToBins | A wrapper function for 'pafAlignmentToBins' binning multiple... |
| parseCigarString | Function to parse CIGAR string into a set interval ranges. |
| pipe | Pipe operator |
| plotAVA | Plot all-versus-all alignments stored in PAf format. |
| plotGenome | Visualize genome-wide PAF alignments. |
| plotMiro | Visualize PAF alignments. |
| plotSelf | Make a horizontal sequence self-alignments. |
| processPafTags | Process PAF specific alignment tags. |
| q2t | Function to convert coordinates between different coordinate... |
| readPaf | Read PAF from an input file |
| regions2FASTA | Export FASTA sequences from a set of Genomic Ranges. |
| reportGaps | Report gaps between a set of target and query ranges. |
| simpledotplot | Plot simple dotplot of two sequences. |
| StatMiropeats | A ggproto class definition to extend the functionality of... |
| StatWideArc | A ggproto class definition to extend the functionality of... |
| subsetPaf | Subset PAF alignments at desired genomic range. |
| subsetPafAlignments | Subset PAF alignments at desired genomic range. |
| syncRangesDir | Synchronize orientation of genomic ranges given the desired... |
