![[R logo]](http://stat.ethz.ch/R-manual/R-devel/doc/html/Rlogo.svg)
![[Up]](http://stat.ethz.ch/R-manual/R-devel/doc/html/left.jpg)
![[Top]](http://stat.ethz.ch/R-manual/R-devel/doc/html/up.jpg)
| build.plotter | Generating plotters |
| build.plotter.advanced | Generating plotters |
| build.plotter.basic | Generating plotters |
| build.plotter.colorByGroup | Generating plotters |
| build.plotter.colorByLane | Generating plotters |
| build.plotter.colorBySample | Generating plotters |
| build.plotter.colorByX | Generating plotters |
| build.plotter.highlightSample | Generating plotters |
| build.plotter.highlightSample.colorByLane | Generating plotters |
| completeAndCheckDecoder | Reading QC results data |
| get.size.factors | Get summary data tables |
| get.summary.table | Get summary data tables |
| makeMultiPlot | Generating summary multi-plots |
| makeMultiPlot.all | Generating all default plots |
| makeMultiPlot.basic | Generating summary multi-plots |
| makeMultiPlot.colorByGroup | Generating summary multi-plots |
| makeMultiPlot.colorByLane | Generating summary multi-plots |
| makeMultiPlot.colorBySample | Generating summary multi-plots |
| makeMultiPlot.highlightSample | Generating summary multi-plots |
| makeMultiPlot.highlightSample.all | Generating sample highlight multi-plots |
| makeMultiPlot.highlightSample.colorByLane | Generating summary multi-plots |
| makeMultiPlot.highlightSample.colorByLane.all | Generating sample highlight multi-plots |
| makeMultiPlot.withPlotter | Generating summary multi-plots |
| makePlot.biotype.rates | Plot Biotype rates |
| makePlot.chrom.type.rates | Chromosome type rate plot |
| makePlot.cigarLength.distribution | Plot the length distribution of a given cigar operation |
| makePlot.cigarOp.byCycle | Plot Cigar Operator Rate |
| makePlot.clipping | Plot Alignment Clipping |
| makePlot.dropped.rates | Read Drop Plot |
| makePlot.gc | Plot GC content |
| makePlot.gene.assignment.rates | Gene assignment rate plot |
| makePlot.gene.cdf | Plot the cumulative gene diversity curve |
| makePlot.genebody | Plot Gene-Body coverage distribution |
| makePlot.genebody.coverage | Plot Gene-Body coverage distribution |
| makePlot.genebody.coverage.lowExpress | Plot Gene-Body coverage distribution |
| makePlot.genebody.coverage.UMQuartile | Plot Gene-Body coverage distribution |
| makePlot.insert.size | Plot Insert Size Distribution. |
| makePlot.legend.box | Plot legend |
| makePlot.legend.over | Plot legend |
| makePlot.mapping.rates | Plot mapping rates |
| makePlot.minus.clipping.NVC | Nucleotide-rate by read cycle plot |
| makePlot.missingness.rate | Plot N-Rate by read cycle |
| makePlot.norm.factors | Plot Alignment Clipping |
| makePlot.norm.factors.vs.TC | Plot Alignment Clipping |
| makePlot.NVC | Nucleotide-rate by read cycle plot |
| makePlot.NVC.clip.matchByClipPosition | Plot clipped nucleotide rates, aligned by the distance from the point of clipping. |
| makePlot.NVC.lead.clip | Clipped sequence nucleotide-by-position plot |
| makePlot.NVC.lead.clip.matchByClipPosition | Plot clipped nucleotide rates, aligned by the distance from the point of clipping. |
| makePlot.NVC.tail.clip | Clipped sequence nucleotide-by-position plot |
| makePlot.NVC.tail.clip.matchByClipPosition | Plot clipped nucleotide rates, aligned by the distance from the point of clipping. |
| makePlot.onTarget.counts | On-Target Rates |
| makePlot.onTarget.rates | On-Target Rates |
| makePlot.overlap | Overlap Mismatch Rates |
| makePlot.overlap.coverage | Overlap Mismatch Rates |
| makePlot.overlapMismatch.byBase | Overlap Mismatch Rates |
| makePlot.overlapMismatch.byBase.atScore | Overlap Mismatch Rates |
| makePlot.overlapMismatch.byCycle | Overlap Mismatch Rates |
| makePlot.overlapMismatch.byQual.min | Overlap Mismatch Rates |
| makePlot.overlapMismatch.byQual.read | Overlap Mismatch Rates |
| makePlot.overlapMismatch.perRead | Overlap Mismatch Rates |
| makePlot.overlapMismatch.size | Overlap Mismatch Rates |
| makePlot.qual.pair | Plot quality score by read cycle |
| makePlot.raw.NVC | Nucleotide-rate by read cycle plot |
| makePlot.readLengthDist | Plot the distribution of read lengths. |
| makePlot.reference | Plot Reference Mismatch Rates |
| makePlot.referenceMismatch | Plot Reference Mismatch Rates |
| makePlot.referenceMismatch.byBase | Plot Reference Mismatch Rates |
| makePlot.referenceMismatch.byBase.atScore | Plot Reference Mismatch Rates |
| makePlot.referenceMismatch.byCycle | Plot Reference Mismatch Rates |
| makePlot.referenceMismatch.byScore | Plot Reference Mismatch Rates |
| makePlot.referenceMismatch.perRead | Plot Reference Mismatch Rates |
| makePlot.runTimePerformance | Chromosome type rate plot |
| makePlot.splice.junction.event | Plot Splice Junction Event Rates |
| makePlot.splice.junction.event.counts | Plot Splice Junction Event Rates |
| makePlot.splice.junction.event.proportions | Plot Splice Junction Event Rates |
| makePlot.splice.junction.event.proportionsByType | Plot Splice Junction Event Rates |
| makePlot.splice.junction.event.ratesPerRead | Plot Splice Junction Event Rates |
| makePlot.splice.junction.loci.counts | Splice Junction Loci Count Plot |
| makePlot.strandedness.test | Strandedness Test Plot |
| makePlot.targetDistribution | On-Target Rates |
| plotter | Generating plotters |
| QoRTs.default.plotting.params | Generating plotters |
| read.qc.results.data | Reading QC results data |