| +-method |
Combines 2 AbSeqCRep objects together for comparison |
| +-method |
Combines a AbSeqCRep object with a AbSeqRep object together for comparison |
| +-method |
Combines a AbSeqRep object with a AbSeqCRep object together for comparison |
| +-method |
Combines 2 AbSeqRep objects together for comparison |
| .abundanceAnalysis |
Conducts abundance analysis |
| .abundancePlot |
Abundance distribution |
| .alignQualityHeatMaps |
Plots all 5 alignment quality heatmaps |
| .allPrimerNames |
Collect primer names from FASTA |
| .aminoAcidBar |
Plots amino acid composition logo |
| .aminoAcidPlot |
Composition logo plot |
| .analyzeUpstreamValidity |
Plots the validity of upstream sequences |
| .annotAnalysis |
Annotation analysis |
| .asRepertoireAlignLen |
Accessor for 'alignlen' slot |
| .asRepertoireBitscore |
Accessor for 'bitscore' slot |
| .asRepertoireChain |
Accessor for 'chain' slot |
| .asRepertoireDir |
Accessor for the 'outdir' slot |
| .asRepertoireList |
Accessor for AbSeqCRep's list of AbSeqRep objects |
| .asRepertoireName |
Accessor for the 'name' slot |
| .asRepertoirePrimer3 |
Accessor for the 'primer3end' slot |
| .asRepertoirePrimer5 |
Accessor for the 'primer5end' slot |
| .asRepertoireQueryStart |
Accessor for 'qstart' slot |
| .asRepertoireSubjectStart |
Accessor for 'sstart' slot |
| .asRepertoireUpstream |
Accessor for the 'upstream' slot |
| .boxPlot |
Creates a box plot |
| .calculateDInd |
Calculates the "standard" diversity indices |
| .calculateDiversityEstimates |
Calculates Lower Bound Estimates for unseen species and Common Diversity Indices from clonotype tables |
| .canonicalizeTitle |
Convert file names to human friendly text |
| .capitalize |
Helper function to capitalize the first letter of 'str' |
| .checkVert |
Checks if abseqPy has a metadata line that suggests the orientation |
| .cloneDistHist |
Marginal histogram of clonotypes (blue for shared, grey for total). The y axis is scaled by sqrt (but it doesn't really matter anyway, since we're stripping away the y-ticks) |
| .cloneDistMarginal |
Marginal density graph of clonotypes (blue for shared, grey for total, purple for exclusive clones) |
| .clonotypeAnalysis |
Comprehensive clonotype analyses |
| .collateReports |
Collate all HTML reports into a single directory and cretate an entry 'index.html' file that redirects to all collated HTML files |
| .commonPrimerNames |
Collect the intersection of all primer names within a collection of primer files |
| .correlationTest |
Conducts pearson and spearman correlation analysis on dataframe |
| .distanceMeasure |
Computes the distance between pariwise samples |
| .diversityAnalysis |
Title Diversity analysis |
| .emptyPlot |
Creates and returns an empty plot |
| .findRepertoires |
Given a directory = <abseqPy_outputdir>/RESULT_DIR/, returns the directories (repositories) in 'directory'. That is, will not return any sample_vs_sample directories. This is done by asserting that a 'repository' must have an (analysis.params) file, and a summary.txt file. |
| .generateAllSpectratypes |
Generates all FR/CDR spectratypes |
| .generateDelayedReport |
Generates report for all samples in 'compare' |
| .generateReport |
Generates HTML report from 'AbSeqRep' and 'AbSeqCRep' ojects |
| .getLineTypes |
Helper function to return line types by importance based on provided CD/Fs regions |
| .getTotal |
Get total number of samples (n) |
| .hmFromMatrix |
Plots a plotly heatmap from provided matrix |
| .inferAnalyzed |
Returns all samples found under 'sampleDirectory' |
| .loadMatrixFromDF |
Given a dataframe with the columns "from", "to", and value.var, return a symmetric matrix (with diagonal values = diag). I.e. a call to isSymmetric(return_value_of_this_function) will always be TRUE. |
| .loadSamplesFromString |
Loads AbSeqCRep or AbSeqRep objects from a list of sampleNames |
| .pairwiseComparison |
Conduct all vs all pairwise comparison analyses |
| .plotCirclize |
V-J association plot |
| .plotDist |
Bar plotter |
| .plotDiversityCurves |
Plots rarefaction, recapture, and de-dup plots for specified 'region' |
| .plotDuplication |
Duplication level plot |
| .plotErrorDist |
Plots the error distribution for each region: CDRs, FRs, IGV, IGD, and IGJ |
| .plotIGVErrors |
Plots the error distribution for IGV germlines |
| .plotIGVUpstreamLenDist |
Plot IGV family distribution for a given 'upstreamLengthRange' |
| .plotIGVUpstreamLenDistDetailed |
Plots the detailed length distribution for IGV families |
| .plotPrimerIGVStatus |
Plots, for a given 'category' and 'pend', the 'primer' IGV indelled distribution in a bar plot |
| .plotPrimerIntegrity |
Plots the distribution of primer integrity for a given 'category' and 5' or 3' 'pend' |
| .plotRarefaction |
Rarefaction plot |
| .plotRecapture |
Plots capture-recapture |
| .plotSamples |
Monolith AbSeq Plot function - the "driver" program |
| .plotSpectratype |
Spectratype plotter |
| .plotUpstreamLength |
Plot upstream distribution |
| .plotUpstreamLengthDist |
Plot upstream sequence length distribution for upstream sequences (5'UTR or secretion signal) for a given 'upstreamLengthRange' |
| .primerAnalysis |
Conducts primer specificity analysis |
| .prodDistPlot |
Plots a distribution plot for different productivity analysis files |
| .productivityAnalysis |
Conducts productivty analysis |
| .productivityPlot |
Summary of productivity |
| .readSummary |
Return value specifed by key from AbSeq's summary file |
| .regionAnalysis |
Title Shows varying regions for a given clonotype defined by its CDR3 |
| .reportLBE |
Reports abundance-based (Lower bound) diversity estimates using the Vegan package |
| .saveAs |
Saves ggplot object as a Rdata file. |
| .scatterPlot |
Title Creates a scatter plot |
| .scatterPlotComplex |
Creates a complex scatter plot |
| .secretionSignalAnalysis |
Secretion signal analysis |
| .substituteStringInFile |
Substitutes the first occurance of 'key' with 'value' in 'filename' |
| .summarySE |
Summary of dataframe |
| .topNDist |
Title Clonotype table |
| .UTR5Analysis |
5' UTR analysis |
| .vennIntersection |
Title Creates Venndiagram for clonotype intersection |
| AbSeqCRep |
S4 class - AbSeqCompositeRepertoire analysis object |
| AbSeqCRep-class |
S4 class - AbSeqCompositeRepertoire analysis object |
| AbSeqRep |
S4 class - AbSeqRepertoire analysis object |
| AbSeqRep-class |
S4 class - AbSeqRepertoire analysis object |
| abseqReport |
Visualize all analysis conducted by abseqPy |
| report |
Plots AbSeqRep or AbSeqCRep object to the specfied directory |
| report-method |
Plots AbSeqRep or AbSeqCRep object to the specfied directory |
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