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Gallery

Find the plot for the question you are asking of your data: start from what the data describes, or from the file you already have.

Every figure here is drawn by karyon in your browser, in this page's light or dark. On the pages they lead to, drag a figure along its genome, zoom it with the buttons under it or a pinch, and hover a mark for what it holds.

Browse by what you want to show

  • A read depth profile with a dropout, a reference band, the rpoB gene with its resistance-determining region, and variant lollipops, all on one axis

    Signal and sequence A value or a symbol at every position: depth, windowed statistics, methylation by strand, the reference bases, logos and per-base attribution.

  • Three transcription units over the ESX-1 genes of M. tuberculosis, each a bent arrow at its start site with a hairpin or a bar at its end, above the gene models they carry

    Annotation and coordinates Genes, transcription units and reading frames, with rulers in bases or codons and a key to the colours.

  • An association scan over rpoB whose peak crosses the threshold line, the gene beneath it, and a genotype matrix of the isolates at the associated sites

    Variation and association From one call to a cohort: point and structural variants, copy number, variable sites, genotype matrices, association scans and site-wise selection.

  • Reads packed into rows under a depth profile and a candidate SNV, coloured by strand, with mismatches painted against the reference, a deletion, an insertion, faded low-quality reads and a count of the reads not shown

    Reads and molecules The evidence one molecule at a time: pileups, split reads, per-read methylation, splice junctions and raw nanopore current.

  • Two M. tuberculosis chromosomes compared as a dotplot, where an inversion runs as an anti-diagonal and a translocated block sits off the main diagonal, above the same alignment drawn as ribbons

    Comparisons and alignments Two or more sequences compared: alignments, domain architectures, dotplots, synteny ribbons and gene neighbourhoods.

  • Four radial views of one outbreak tree: a circular time tree with country and depth rings, a fan with a collapsed clade, time radiating inwards, and a circular cladogram

    Phylogeny and clades Trees in every layout with their metadata, two trees face to face, spans painted onto clades, and a tree around a map.

  • An eight-panel synthetic atlas of tree geometries, ancestral states, selection on branches and at sites, a tanglegram, a population trajectory and lineage frequencies through time

    Evolution and surveillance Results fitted upstream: ancestral states, selection on branches and at sites, population trajectories and lineage counts through time.

  • The 4.41 Mb H37Rv chromosome as concentric rings of genes, GC content and GC skew, with resistance mutations marked and chords across the middle joining the ends of two rearrangements

    Whole genomes and maps Context beyond one locus: an ideogram, a whole assembly, a circular genome and a world map.

Choose from the shape of your data

Find the file you have: the plot links to its reference and names the command line flag that draws it, and the route opens its page in this gallery.

Your data Start with Route
Aligned reads: a BAM, or SAM text as samtools view writes it Read pileup, --pileup Reads and molecules
Reads aligned in pieces: a BAM or SAM with SA tags Split reads, --split-reads Reads and molecules
Splice junction counts: STAR's SJ.out.tab Splice junctions, --junctions Reads and molecules
Methylation calls read by read: a Bismark methylation extractor file Methylation by molecule, --bisulfite Reads and molecules
Raw nanopore current and a basecaller move table Nanopore signal Reads and molecules
A value per base: bedGraph, samtools depth, a column of values, or the depth of a BAM Coverage, --coverage Signal and sequence
A statistic in windows: bedGraph Windowed statistic, --windows Signal and sequence
Modified bases per strand: bedMethyl from modkit pileup Methylation by strand, --methylation Signal and sequence
Per-base model attribution: bedGraph, plus the reference as FASTA Per-base attribution, --dynseq with --with-sequence Signal and sequence
Aligned sequences of a motif: aligned FASTA Sequence logo, --logo Signal and sequence
A reference sequence: FASTA Reference sequence, --sequence, or six reading frames, --orfs Signal and sequence, Annotation and coordinates
Genes and other intervals: BED, GFF3 or GTF Features, --features Annotation and coordinates
Point calls: VCF Point variants, --variants Variation and association
Structural calls: VCF with symbolic alleles or SVTYPE Structural variants, --structural Variation and association
Copy number segments: CNVkit .cns, ASCAT or .seg Copy number, --copy-number with --ploidy Variation and association
Closely related genomes: aligned FASTA Variable sites, --snps, or a multiple alignment, --msa Variation and association, Comparisons and alignments
The genotypes of a cohort: VCF with samples Genotypes by sample, --genotypes Variation and association
A value per sample per site: a table Genotype matrix, --matrix Variation and association
Association statistics: a table of position and value Association scan, --manhattan Variation and association
Site-wise results from a codon model Site-wise selection Variation and association, Evolution and surveillance
A pairwise alignment: PAF from minimap2 Dotplot, --dotplot, or synteny ribbons, --synteny Comparisons and alignments
Protein domains: an InterProScan table Domain architectures, --domains Comparisons and alignments
Genes from several genomes, and the hits between them Gene neighbourhoods, --loci with --links Comparisons and alignments
A phylogeny: Newick, with or without BEAST and NHX annotations Annotated tree, --tree Phylogeny and clades
Two trees over the same taxa Tanglegram, --tanglegram with --against Phylogeny and clades
Spans carried by named taxa: Gubbins GFF3, and the tree Clade blocks, --clades with --with-tree Phylogeny and clades
Ancestral states, branch events or branch ω, as tree annotations Ancestral states and branch events, Rust only Evolution and surveillance
Estimates through time, such as effective population size or R Phylodynamic trajectory Evolution and surveillance
Lineage counts and totals through time Lineage surveillance Evolution and surveillance
Cytogenetic bands: a UCSC cytoBand table Ideogram, --ideogram Whole genomes and maps
An assembly of many contigs or chromosomes Whole assembly, Rust only Whole genomes and maps
A circular chromosome or plasmid Circular genome, --circular Whole genomes and maps
A latitude and longitude per sample Map, Rust only Whole genomes and maps

BAM, BCF, compressed files and CRAM

A BAM file, a BCF and anything compressed with gzip or bgzip (.vcf.gz, .gff3.gz) are read as they are. CRAM comes in through a pipe: samtools view writes the text these readers take, and a track file can be - for standard input. See compressed and binary files.

Tracks and drawings

Most plots here are tracks: bands that stack over one shared coordinate axis, so any of them can sit above or below any other. The circular genome, the map and the tree around a map are drawings instead (Rings, Map and PhyloMap), each with a coordinate system of its own, and a Panels sheet puts drawings and figures side by side.

Every track in one place

  • Track catalogue

    All 38 track types, family by family, with the options of each and the files it reads.

  • Recipes

    Complete programs that stack several of these plots into one figure.

  • Command line

    Every flag, and how the order of the flags becomes the order of the stack.

Every figure in this gallery is drawn by a program in the repository's examples/ directory, so the code behind each one is there to read and copy.