Package index • SeqPlotR

All functions

LegendKey(): Legend Key
aes(): Capture evaluated constant aesthetics
create_genome_windows(): Build genome windows from region strings
cytoband_hg38: UCSC hg38 cytoband table
default_genome_windows(): Default whole-genome windows
flexoki_palette(): Load colors from Kepano's Flexoki palette
is_seq_file_conn(): Test whether x is a SeqPlotR file connection
is_seq_legend_spec(): Test if an object is a SeqLegendSpec
load_cytobands(): Load a cytoband annotation table
map(): Capture unevaluated mapping expressions
`%|%`: Append a track to the current row (horizontal stacking)
`%||%`: Null-coalescing operator
`%+%`: Add a track, element, or plot-level feature to a SeqPlot or SeqTrack
`%__%`: Start a new row (vertical stacking)
open_bam(): Open a BAM file connection
open_bigwig(): Open a bigWig file connection
open_h5(): Open a .cool or .mcool HDF5 contact matrix file
open_hic(): Open a .hic file connection (Juicer format)
print(<SeqPlot>): Auto-print a SeqPlot
seq_arc(): Bezier arch link between two genomic loci on the same track
seq_arch(): Bezier arch with vertical stems
seq_area(): Draw filled area under a curve
seq_bar(): Draw bars
seq_blank(): Return a blank plot-level placeholder
seq_chip(): ChIP-style multi-track signal + peaks plot
seq_cn_heatmap(): Multi-sample copy-number heatmap
seq_copynumber(): Copy-number scatter plot
seq_curve(): Draw bezier curves
seq_density(): Draw a kernel density estimate as a filled area
seq_gene(): Draw gene models
seq_gradient_legend(): Create a color gradient (color-bar) legend specification
seq_hic(): Hi-C contact matrix
seq_highlight(): Cross-track region highlight band
seq_ideogram(): Chromosome ideogram from cytogenetic bands
seq_legend(): Create a legend placement specification
seq_line(): Draw a line
seq_lollipop(): Draw lollipops
seq_path(): Draw connected paths
seq_plot(): Create a new seq_plot
seq_point(): Draw points
seq_poly(): Draw filled polygons
seq_preview_circos(): Preview a SeqPlotR plot as a circos layout
seq_preview_layout(): Preview the grid layout of a SeqPlotR plot
seq_reads(): IGV-style read alignment track element
seq_recon(): Strand-classified SV reconstruction arches
seq_resolve(): Compose wrapper-built plots into a parent plot
seq_ribbon(): Draw a filled ribbon between two y series
seq_scale_color_continuous() seq_scale_fill_continuous(): Continuous color scale for SeqAes mappings
seq_scale_color_discrete() seq_scale_fill_discrete(): Discrete color scale for SeqAes mappings
seq_scale_continuous(): Continuous position scale
seq_scale_discrete(): Discrete position scale
seq_scale_genomic(): Genomic position scale
seq_scalebar(): Reference scalebar element
seq_segment(): Draw line segments
seq_sequence(): IGV-style nucleotide sequence track element
seq_string(): Cubic-Bezier string link between two genomic loci
seq_synteny(): Filled trapezoid connecting two tracks
seq_text(): Draw text labels
seq_tile(): Draw tiles (rectangles or rotated diamonds)
seq_track(): Create a new seq_track
seq_zoom(): Zoom / highlight polygon between two tracks