Function reference • splicejam

Splicejam core functions These functions are the heart of the splicejam package
`exoncov2polygon()`	Convert exon coverage to polygons
`gene2gg()`	Gene GRangesList to ggplot2 grob
`grl2df()`	GRangesList to data.frame for ggplot2
`make_ref2compressed()`	Create a ref2compressed function to compress GR gaps
`plotSashimi()`	Jam Sashimi plot
`prepareSashimi()`	Prepare Sashimi plot data
RNA-seq functions Functions aimed at RNA-seq analysis
`assignGRLexonNames()`	Assign exon names to GRangesList
`closestExonToJunctions()`	Find closest exon to splice junction ends
`combineGRcoverage()`	Combine GRanges coverage replicates
`defineDetectedTx()`	Define detected transcripts
`detectedTxInfo()`	Summarize detected transcript results
`exoncov2polygon()`	Convert exon coverage to polygons
`flattenExonsBy()`	Flatten exons by gene or transcript
`getGRcoverageFromBw()`	Get coverage for GRanges from bigWig files
`groups2contrasts()`	Define experimental contrasts from sample groups
`internal_junc_score()`	maximum overlapping internal junction score
`makeTx2geneFromGtf()`	Make tx2gene data.frame from a GTF file
`make_ref2compressed()`	Create a ref2compressed function to compress GR gaps
`prepareSashimi()`	Prepare Sashimi plot data
`runDiffSplice()`	Perform differential isoform analysis using diffSplice
`sortSamples()`	Sort biological sample labels for experimental design
`spliceGR2junctionDF()`	Splice junction data.frame summary
Splicejam R-shiny functions Functions to enable Splicejam R-shiny
`launchSashimiApp()`	Launch Sashimi R-shiny application
`sashimiAppConstants()`	Sashimi Shiny app constants
`sashimiAppServer()`	Sashimi Shiny app server
`sashimiAppUI()`	Sashimi Shiny app UI
`sashimiDataConstants()`	Prepare sashimi plot required data
ALE-specific RNA-seq functions Functions specific to ALE (alternate last exon) RNA-seq analysis
`ale2violin()`	Prepare ALE data for violin plots
`getFirstStrandedFromGRL()`	Get first stranded GRanges feature per GRangesList
`tx2ale()`	tx2ale: detect alternative last exons (ALE) from transcript data
RNA-seq codon usage functions Functions specific to codon usage in RNA-seq analysis
`codonUsage2df()`	Make codon usage data.frame
`dna2codon()`	Convert DNA to 3-base codons
`jamCai()`	Calculate Codon Adaptation Index
GRanges functions Functions to manipulate the Genomic Ranges (GRanges) family of objects
`addGRLgaps()`	Add gaps between GRangesList regions
`addGRgaps()`	Add gaps between GRanges regions
`annotateGRLfromGRL()`	Annotate GRangesList from GRangesList objects
`annotateGRfromGR()`	Annotate GRanges using another GRanges object
`assignGRLexonNames()`	Assign exon names to GRangesList
`closestExonToJunctions()`	Find closest exon to splice junction ends
`combineGRcoverage()`	Combine GRanges coverage replicates
`exoncov2polygon()`	Convert exon coverage to polygons
`findOverlapsGRL()`	Find overlaps between two GRangesList objects
`flattenExonsBy()`	Flatten exons by gene or transcript
`getFirstStrandedFromGRL()`	Get first stranded GRanges feature per GRangesList
`getGRLgaps()`	Get gaps in GRangesList objects
`getGRcoverageFromBw()`	Get coverage for GRanges from bigWig files
`getGRgaps()`	Get gaps in GRanges
`grl2df()`	GRangesList to data.frame for ggplot2
`jam_isDisjoint()`	Test whether GRanges are disjoint (non-overlapping)
`make_ref2compressed()`	Create a ref2compressed function to compress GR gaps
`sortGRL()`	Sort GRangesList elements by chromosome and position
`spliceGR2junctionDF()`	Splice junction data.frame summary
`stackJunctions()`	Stack the y-axis position of junctions
Design functions Functions aimed at manipulation of experimental design
`curateDFtoDF()`	Curate data.frame into a data.frame
`curateVtoDF()`	Curate vector into a data.frame
`groups2contrasts()`	Define experimental contrasts from sample groups
Plot functions Functions that assist with R plotting
`bgaPlotly3d()`	Create an interactive 3-D BGA plotly visualization
`factor2label()`	Convert factor to a factor label
`gene2gg()`	Gene GRangesList to ggplot2 grob
`grl2df()`	GRangesList to data.frame for ggplot2
`jitter_norm()`	Apply jitter using normal distribution
`plotSashimi()`	Jam Sashimi plot
`prepareSashimi()`	Prepare Sashimi plot data
`stackJunctions()`	Stack the y-axis position of junctions
ggplot2 functions Functions specific to ggplot2 visualization
`gene2gg()`	Gene GRangesList to ggplot2 grob
`stat_diagonal_wide_arc()` `geom_diagonal_wide_arc()`	Draw an area defined by an upper and lower diagonal into an arc
`plotSashimi()`	Jam Sashimi plot
`splicejam-extensions`	splicejam extensions to ggforce
`to_basic(<GeomShape>)`	Support plotly for GeomShape
List functions Functions that assist with list manipulation
`intercalate()`	Intercalate list values into a vector
`list2im()`	Convert list to incidence matrix
String functions Functions aimed at manipulation of character strings
`escapeWhitespaceRegexp()`	Escape whitespace in regular expression patterns
`sortSamples()`	Sort biological sample labels for experimental design
`strsplitOrdered()`	Split the elements of an ordered factor vector
Spatial functions Functions that assist with spatial data, particularly 3-D coordinates
`bgaPlotly3d()`	Create an interactive 3-D BGA plotly visualization
`compressPolygonM()`	Compress genome coordinates of a matrix of polygons
`dfWide2segments()`	Convert data.frame to plotly line segment format
`simplifyXY()`	Simplify XY coordinates to minimal line segments
`spline3d()`	Calculate a spline curve fit in 3-D
Color functions Functions that assist with color manipulation
`df2colorSub()`	Convert data.frame to categorical colors
Matrix functions Functions aimed at manipulation of matrix data
`shrinkMatrix()`	Shrink numeric matrix by groups of rows
Numeric functions Functions aimed at manipulation of numeric data
`geomean()`	Classical geometric mean
`jamGeomean()`	Modified geometric mean for positive and negative values
splicejam test data R data with exons, coverage, and splice junctions
`test_cov_gr`	Sample exon coverage data GRanges
`test_cov_wide_gr`	Sample exon coverage data GRanges with wide introns
`test_exon_gr`	Sample exon data GRanges
`test_exon_wide_gr`	Sample exon data GRanges with wide introns
`test_junc_gr`	Sample junction data GRangesList
`test_junc_wide_gr`	Sample junction data GRangesList with wide introns
Import functions Functions to import specific data formats
`import_juncs_from_bed()`	Import splice junction data from BED or SJ.out.tab file
`psl2df()`	Convert PSL alignment to data.frame

Reference

Splicejam core functions

RNA-seq functions

Splicejam R-shiny functions

ALE-specific RNA-seq functions

RNA-seq codon usage functions

GRanges functions

Design functions

Plot functions

ggplot2 functions

List functions

String functions

Spatial functions

Color functions

Matrix functions

Numeric functions

splicejam test data

Import functions