Advanced visualizations¶

An advanced visualization is a domain chart that knows what its columns mean. A volcano knows it needs a feature, an effect size and a significance; a genome view knows chromosome and position. You bind your columns to those roles once, and the tile brings the domain logic: thresholds, tiers, genomic axes, linked selections.

Pick one over a generic Figure when your table matches a known shape (the output of DESeq2, mosdepth, QIIME2, AlphaFold...). Pick a Figure for a plain plot of any columns.

Catalog¶

Click a thumbnail to enlarge it, or a name to jump to its entry.

Differential analysis

Volcano v0.13.0+

Group compare v1.13.0+

DA barplot v0.13.0+

GSEA running score v1.11.0+

Single cell & embeddings

Embedding v0.13.0+

Dot plot v0.13.0+

Knee plot v1.13.0+

Genome tracks

Coverage track v0.13.0+

Genome view v1.13.0+

Sashimi v1.11.0+

Copy-number profile v1.13.0+

Contact map v1.13.0+

Transcript structure v1.13.0+

Gene arrow track v1.11.0+

Variants & rearrangements

Oncoplot v0.13.0+

Manhattan v0.13.0+

Lollipop v0.13.0+

Genome chord v1.13.0+

Fusion structure v1.11.0+

Signal & read profiles

Profile v1.11.0+

Signal matrix v1.11.0+

Damage profile v1.13.0+

Microbiome & ecology

Sunburst v0.13.0+

Stacked taxonomy v0.13.0+

Rarefaction v0.13.0+

Phylogenetic tree v0.13.0+

Samples & specimens

Allele grid v1.20.0+

Pedigree v1.20.0+

Ideogram v1.20.0+

Spatial cells v1.20.0+

General purpose

Scatter (X/Y) v1.11.0+

UpSet v0.13.0+

Parallel coordinates v1.13.0+

Record card v1.13.0+

Hierarchical heatmap v0.13.0+

Sankey v0.13.0+

Ranked table v1.20.0+

Ranked distribution v1.20.0+

Benchmarking

PR benchmark v1.10.0+

Confusion matrix v1.10.0+

Metric with CI v1.10.0+

Proteins

3D structure v1.19.0+

Sequence track v1.19.0+

Alignment v1.19.0+

HMM logo v1.19.0+

Domain architecture v1.19.0+

Secondary structure v1.19.0+

Predicted aligned error v1.19.0+

Ramachandran v1.19.0+

How to use one¶

In the dashboard editor, add a component, pick a data collection, then the Advanced viz type.
Pick a kind. The builder ranks the kinds by how well they fit the collection (see the kind picker).
Bind each role to a column under Column bindings. Required roles must be bound; the builder checks the column types.
Optionally choose where the controls go under Viz controls, then add the tile.

In a dashboard YAML file, the same tile is a component_type: advanced_viz entry. A role x binds through the config key x_col:

- tag: viz-de
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: de_results
  viz_kind: volcano
  config:
    viz_kind: volcano
    feature_id_col: gene_id
    effect_size_col: log2FoldChange
    significance_col: padj

Every entry below follows the same layout: a version badge (v1.19.0+ means available since that release), a screenshot, its input table (one row per column: the Column name as in its YAML example, the Config key that binds it, its Need (required or optional), the Type checked and an Example value), the tools whose output fits, its controls and a YAML example.

Shared settings¶

Controls and where they go¶

Each tile splits its controls in two tiers. Primary controls change what is shown: the view switch, thresholds, colour by, a gene or sample picker. Cosmetic controls change how it is drawn: marker sizes, palettes, labels, legend. The config key controls_placement sets where they go v1.13.0+:

`controls_placement`	Where
`popover` (default)	Behind the settings icon, or docked beside or above the plot when the tile has room v1.14.0+
`header`	Primary controls in a strip under the title, cosmetic ones in the popover
`rail`	All controls in a column right of the plot, no popover

popoverheaderrail

A docked panel shows the first three controls and folds the rest under More options. The component-level controls_placement (auto, right, top, popover), the builder's Viz controls section, forces the dock side or keeps the icon.
A reader can move the controls with the placement picker; the choice lasts the session.
A dashboard sets a default for every tile with advanced_viz_controls. See Tile height and control placement.
Every tile also offers Show underlying data: the rows behind the plot.

Switchable views¶

Some kinds draw the same rows several ways. view is the view the tile opens on, views the views it offers. A view is only offered when its columns are bound.

Kind	Views (default first)
Volcano	`volcano`, `ma`, `qq`
Dot plot	`dotplot`, `enrichment`
PR benchmark	`pr`, `roc`, `both`
Coverage track	`track`, `locus`
Copy-number profile	`plotly`, `locus`
Sashimi	`plotly`, `genomespy`

Retired kinds still load

viz_kind: ma, qq, enrichment and roc_pr_curve became views in v1.13.0. They still load and open on the matching view of volcano, dot_plot or pr_benchmark; the builder no longer offers them. ancombc_differentials loads as a DA barplot.

The kind picker¶

The builder lists the tile's current kind first, then Recommended kinds, then the others, folded. A badge says what a suggestion rests on:

Badge	Meaning
Named match	Columns are named for the kind's roles (`log2FoldChange`, `padj`...)
Shape match	Columns have the right types and shape, without matching names
Fits your selection	Another tile on the tab emits a selection the kind can follow, as for a Record card
Weak	Pickable, but a required role has no good column

Differential analysis¶

Volcano¶

v0.13.0+ viz_kind: volcano

Effect size against significance for a differential test. The same table also reads as an MA plot and a QQ plot from the view switch.

Input: one row per gene.

Column	Config key	Need	Type	Example
`gene_id`	`feature_id_col`	required	String	`ENSG00000141510`
`log2FoldChange`	`effect_size_col`	required	Float	`-1.84`, `2.47`
`padj`	`significance_col`	required	Float	`3.2e-08`
`log2_baseMean`	`avg_log_intensity_col`	optional, adds the MA view	Float	`11.2`
`pvalue`	`p_value_col`	optional, adds the QQ view	Float	`1.1e-09`
`gene_name`	`label_col`	optional, hover label	String	`TP53`
`contrast`	`category_col`	optional, point colour	String	`treated_vs_control`

Compatible inputs: DESeq2, limma or edgeR results tables, as nf-core/differentialabundance publishes them.

Controls

Primary: View (Volcano, MA, QQ), p / padj threshold, |effect| or |log2 FC| threshold, Top-N labels, Search
Cosmetic: Show top-N labels; in the QQ view: identity line, 95% null band, point size

Contrasts v1.19.2+: reference, contrast_prefix and contrast_separator name the two sides (localityBarcelona reads Barcelona, _vs_ names both), effect_label can say vs {reference}, group_symbols and marker_cols set the marker shape and the Shape by control, hover_col and hover_category add hover lines.

YAML

- tag: viz-volcano
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: de_results
  viz_kind: volcano
  config:
    viz_kind: volcano
    feature_id_col: gene_id
    effect_size_col: log2FoldChange
    significance_col: padj
    avg_log_intensity_col: log2_baseMean
    p_value_col: pvalue
    views: [volcano, ma, qq]

DA barplot¶

v0.13.0+ viz_kind: da_barplot

Ranked signed log fold changes per feature, one panel per contrast or one contrast at a time.

Input: one row per taxon and contrast (long format).

Column	Config key	Need	Type	Example
`taxon`	`feature_id_col`	required	String	`Bacteroides`
`contrast`	`contrast_col`	required	String	`treatment_vs_control`
`lfc`	`lfc_col`	required	Float	`1.92`, `-2.35`
`q_val`	`significance_col`	optional, significance threshold	Float	`0.003`
`label`	`label_col`	optional, display label	String	`B. fragilis`

Compatible inputs: ANCOM-BC, ALDEx2 or MaAsLin2 differentials (nf-core/ampliseq).

Controls

Primary: Contrast tabs (All or one contrast), Top-N per panel, Significance threshold
Cosmetic: None

Contrasts v1.19.2+: reference, contrast_prefix, contrast_separator and group_colors name the two sides as on the Volcano and colour a bar by the group it leans toward; bars past the cutoff are hatched. effect_label, hover_col and hover_category as on the Volcano.

YAML

- tag: viz-da-barplot
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: ancombc_results
  viz_kind: da_barplot
  config:
    viz_kind: da_barplot
    feature_id_col: taxon
    contrast_col: contrast
    lfc_col: lfc
    significance_col: q_val
    contrast_view: all

GSEA running score¶

v1.11.0+ viz_kind: gsea_running_score

The running enrichment score along the ranked gene list, one curve per gene set, with the set members as a rug.

Input: one row per gene set and rank.

Column	Config key	Need	Type	Example
`gene_set`	`gene_set_col`	required	String	`HALLMARK_E2F_TARGETS`
`rank`	`rank_col`	required	Numeric	`1`, `2`
`running_es`	`running_es_col`	required	Float	`0.012`
`member`	`member_col`	optional, the hit rug	Boolean or 0/1	`true`, `false`
`metric`	`metric_col`	optional, ranked metric panel	Float	`3.21`

Compatible inputs: GSEA output of nf-core/differentialabundance.

Controls

Primary: Top-N gene sets, Layout
Cosmetic: Shade the leading edge, Hit rug, Ranked metric

YAML

- tag: viz-gsea-running-score
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: gsea_running
  viz_kind: gsea_running_score
  config:
    viz_kind: gsea_running_score
    gene_set_col: gene_set
    rank_col: rank
    running_es_col: running_es
    member_col: member
    metric_col: metric
    top_n_sets: 5

Group compare¶

v1.13.0+ viz_kind: group_compare

Two groups of rows tested feature by feature on demand, drawn as a volcano over a ranked table. The groups come from the dashboard's selection groups or from group values.

Input: one row per cell or sample, one numeric column per feature (wide format).

Column	Config key	Need	Type	Example
`cell_id`	`index_col`	required	String	`AAACCTGAGAAGGCCT-1`
`CD3E`, `MS4A1`, ...	none, every numeric column	required, each one is tested	Numeric	`2.31`, `0.0`
`cluster`	`group_col`	optional, groups when no selection group is picked	String	`cluster_1`

Compatible inputs: Per-cell matrices from nf-core/scrnaseq, or per-sample normalised counts from nf-core/rnaseq.

Controls

Primary: Group A, Group B, Test (Wilcoxon or t-test)
Cosmetic: log1p before testing, FDR threshold, |log2FC| threshold, Top-N labels

YAML

- tag: viz-group-compare
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: cell_by_gene
  viz_kind: group_compare
  config:
    viz_kind: group_compare
    index_col: cell_id
    group_col: cluster
    test: wilcoxon
    default_group_a: cluster_1
    default_group_b: cluster_2
    auto_run: true

Single cell & embeddings¶

Embedding¶

v0.13.0+ viz_kind: embedding

Samples or cells in 2D or 3D, from precomputed coordinates or a PCA, UMAP, t-SNE or PCoA computed live on the server.

The same kind on a sample PCA, with Point size at 25:

Input: one row per cell or sample.

Column	Config key	Need	Type	Example
`cell_id`	`sample_id_col`	required	String	`AAACCTGAGAAGGCCT-1`
`umap_1`	`dim_1_col`	required	Float	`4.12`
`umap_2`	`dim_2_col`	required	Float	`-1.37`
`cluster`	`cluster_col`	optional	String	`T cells`
`umap_3`	`dim_3_col`	optional, adds the 3D view	Float	`0.58`
`CD3E`	`color_col`	optional, colour by metadata or expression	Numeric or String	`2.31`

With compute_method set, the coordinates are computed from the numeric columns instead.

Compatible inputs: scanpy or Seurat coordinates (nf-core/scrnaseq), or any sample by feature matrix with compute_method set.

Controls

Primary: Method (live mode), View (2D, 3D), Colour by
Cosmetic: Method parameters, plot style, legend, hover columns, point size, outline, density overlay, centroids

YAML

- tag: viz-embedding
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: umap_coords
  viz_kind: embedding
  config:
    viz_kind: embedding
    sample_id_col: cell_id
    dim_1_col: umap_1
    dim_2_col: umap_2
    cluster_col: cluster
    selection_enabled: true

Dot plot¶

v0.13.0+ viz_kind: dot_plot

Marker genes by cluster: size is the fraction expressing, colour the mean expression. The enrichment view draws the same marks over a gene-set table.

Input: one row per cluster and gene (long format).

Column	Config key	Need	Type	Example
`cluster`	`cluster_col`	required	String	`T cells`, `B cells`
`gene`	`gene_col`	required	String	`CD3E`, `MS4A1`
`mean_expression`	`mean_expression_col`	required	Float	`2.14`
`frac_expressing`	`frac_expressing_col`	required	Float	`0.87`

Enrichment view, one row per term:

Column	Config key	Need	Type	Example
`term`	`term_col`	required	String	`HALLMARK_E2F_TARGETS`
`nes`	`nes_col`	required	Float	`2.14`
`padj`	`padj_col`	optional	Float	`0.0012`
`gene_count`	`gene_count_col`	optional	Numeric	`196`
`source`	`source_col`	optional	String	`GO_BP`

Compatible inputs: scanpy aggregates per cluster (sc.get.aggregate); clusterProfiler, GSEA or g:Profiler results for the enrichment view.

Controls

Primary: View (Dot plot, Enrichment); dot plot: Sort genes, Sort clusters, Max genes; enrichment: Source, Top-N pathways, padj threshold, Colour by, Sort terms
Cosmetic: Colourscale, reverse colourscale, max and min dot size, outline, labels

YAML

- tag: viz-dot-plot
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: marker_means
  viz_kind: dot_plot
  config:
    viz_kind: dot_plot
    cluster_col: cluster
    gene_col: gene
    mean_expression_col: mean_expression
    frac_expressing_col: frac_expressing
    views: [dotplot]

Knee plot¶

v1.13.0+ viz_kind: knee_plot

Barcode rank against UMI count, one curve per library, with the cell-calling cutoff.

Input: one row per library and barcode rank.

Column	Config key	Need	Type	Example
`sample`	`sample_col`	required	String	`pbmc_1k`
`rank`	`rank_col`	required	Numeric	`1`, `1250`
`umi_count`	`umi_count_col`	required	Numeric	`48213`, `312`
`is_cell`	`is_cell_col`	optional, the cell-calling cutoff	Boolean or 0/1	`true`, `false`

Compatible inputs: STARsolo, alevin-fry or Cell Ranger barcode counts (nf-core/scrnaseq).

Controls

Primary: Log rank (x), Log UMI count (y)
Cosmetic: Show cell-calling cutoff

YAML

- tag: viz-knee-plot
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: barcode_ranks
  viz_kind: knee_plot
  config:
    viz_kind: knee_plot
    sample_col: sample
    rank_col: rank
    umi_count_col: umi_count
    is_cell_col: is_cell

Genome tracks¶

Coverage track¶

v0.13.0+ viz_kind: coverage_track

Depth or signal along a chromosome, per sample or as a cohort median. The locus view redraws it as a zoomable GenomeSpy track.

Input: one row per sample and bin (or base).

Column	Config key	Need	Type	Example
`chrom`	`chromosome_col`	required	String	`MN908947.3`
`start`	`position_col`	required	Integer	`0`, `100`
`depth`	`value_col`	required	Numeric	`812`
`end`	`end_col`	optional, bins as intervals	Integer	`100`, `200`
`sample`	`sample_col`	optional	String	`SAMPLE_01`
`amplicon`	`category_col`	optional, colour by	String	`nCoV-2019_1`

Compatible inputs: mosdepth per-base or per-bin depth (nf-core/viralrecon, sarek, rnaseq), bigWig-derived bins.

Controls

Primary: View (Track, Locus), Sample layout, Y scale, Smoothing, Chromosomes, Samples
Cosmetic: Mark, Colour by, Show individual traces, gene strip

YAML

- tag: viz-coverage-track
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: depth_bins
  viz_kind: coverage_track
  config:
    viz_kind: coverage_track
    chromosome_col: chrom
    position_col: start
    end_col: end
    value_col: depth
    sample_col: sample
    views: [track, locus]

Genome view¶

v1.13.0+ viz_kind: genome_view

A GenomeSpy track on a chromosome axis: scroll to zoom, drag to pan, brush or type a locus to filter the dashboard by region.

Input: one row per position, or per interval with end.

Column	Config key	Need	Type	Example
`chrom`	`chr_col`	required	String	`chr8`
`start`	`pos_col`	required	Integer	`127735800`
`score`	`score_col`	required	Float	`42.7`
`end`	`end_col`	optional, rows as intervals	Integer	`127736600`
`peak_class`	`category_col`	optional, mark colour	String	`promoter`, `enhancer`
`feature`	`feature_col`	optional, hover name	String	`peak_00412`
`sample`	`sample_col`	optional, one lane per sample	String	`H3K27ac_rep1`

Compatible inputs: Any chr / pos / score table: peaks, depth bins, association scores.

Controls

Primary: Chromosome, Locus or gene
Cosmetic: Mark, point size, opacity, threshold rule, one lane per sample, max lanes, assembly, gene annotation lane, zoom to an incoming region

YAML

- tag: viz-genome-view
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: peaks
  viz_kind: genome_view
  config:
    viz_kind: genome_view
    chr_col: chrom
    pos_col: start
    end_col: end
    score_col: score
    category_col: peak_class
    mark: bar
    assembly: hg38
    default_region: "chr8:127,400,000-128,100,000"

Copy-number profile¶

v1.13.0+ viz_kind: cnv_profile

Log2 ratio per bin with the called segments over it and the B-allele frequency underneath. The locus view draws the allele-specific layout.

Input: one row per bin or called segment, both in one table.

Column	Config key	Need	Type	Example
`sample`	`sample_col`	required	String	`TUMOUR_A`
`chrom`	`chrom_col`	required	String	`chr1`
`start`	`start_col`	required	Numeric	`1000000`
`end`	`end_col`	required	Numeric	`1100000`
`log2`	`log2_col`	required	Numeric	`0.14`, `0.06`
`baf`	`baf_col`	optional, the BAF panel	Float	`0.48`
`segment`	`segment_col`	optional, `segment` rows draw as segments, the rest as bins	String	`bin`, `segment`
`copy_number`	`copy_number_col`	optional	Numeric	`2`
`label`	`label_col`	optional, hover label	String	`TP53`

Compatible inputs: CNVkit, ASCAT or Control-FREEC bins and segments (nf-core/sarek).

Controls

Primary: View (Plotly, Locus), Sample, Chromosome
Cosmetic: log2 axis limit, bin marker size, Show BAF panel, gene lane

YAML

- tag: viz-cnv-profile
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: cnv_bins_segments
  viz_kind: cnv_profile
  config:
    viz_kind: cnv_profile
    sample_col: sample
    chrom_col: chrom
    start_col: start
    end_col: end
    log2_col: log2
    baf_col: baf
    segment_col: segment
    views: [plotly, locus]

Contact map¶

v1.13.0+ viz_kind: contact_map

A binned Hi-C matrix, square or as a triangle under a genome track. Zooming re-reads the best resolution for the window.

Input: one row per pair of bins.

Column	Config key	Need	Type	Example
`chrom`	`chrom1_col`	required	String	`chr1`
`start`	`start1_col`	required	Numeric	`0`
`chrom2`	`chrom2_col`	required	String	`chr1`
`start2`	`start2_col`	required	Numeric	`100000`
`count`	`count_col`	required	Numeric	`2841`, `932`
`resolution`	`resolution_col`	optional, one matrix per resolution	Numeric	`100000`, `500000`
`end`	`end1_col`	optional	Numeric	`100000`
`end2`	`end2_col`	optional	Numeric	`200000`
`sample`	`sample_col`	optional	String	`HeLa_rep1`

Compatible inputs: cooler .mcool pixels dumped per resolution (nf-core/hic).

Controls

Primary: Chromosome, Display (square, triangle), Resolution
Cosmetic: Colour scale, log colour scale, row/column balance, separation drawn

YAML

- tag: viz-contact-map
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: hic_pixels
  viz_kind: contact_map
  config:
    viz_kind: contact_map
    chrom1_col: chrom
    start1_col: start
    chrom2_col: chrom2
    start2_col: start2
    count_col: count
    resolution_col: resolution
    display: triangle

Transcript structure¶

v1.13.0+ viz_kind: transcript_structure

The isoforms of one gene, one lane per transcript, exons as blocks and coding parts taller.

Input: one row per exon or CDS block.

Column	Config key	Need	Type	Example
`transcript_id`	`transcript_id_col`	required	String	`ENST00000269305`
`gene_id`	`gene_id_col`	required	String	`ENSG00000141510`
`chrom`	`chrom_col`	required	String	`chr17`
`start`	`start_col`	required	Numeric	`7661779`
`end`	`end_col`	required	Numeric	`7662014`
`feature`	`feature_col`	required	String	`exon`, `CDS`
`strand`	`strand_col`	required	String	`-`
`transcript_class`	`transcript_class_col`	optional, lane colour	String	`known`, `novel`
`sample`	`sample_col`	optional	String	`WT_REP1`
`gene_name`	`gene_name_col`	optional	String	`TP53`
`expression`	`expression_col`	optional, bar beside each lane	Numeric	`12.4`

Compatible inputs: StringTie or bambu GTF exon and CDS rows (nf-core/nanoseq, rnaseq).

Controls

Primary: Gene, Sample, Colour lanes by
Cosmetic: Colour scale, bar beside each lane, isoforms drawn

YAML

- tag: viz-transcript-structure
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: transcript_blocks
  viz_kind: transcript_structure
  config:
    viz_kind: transcript_structure
    transcript_id_col: transcript_id
    gene_id_col: gene_id
    chrom_col: chrom
    start_col: start
    end_col: end
    feature_col: feature
    strand_col: strand
    transcript_class_col: transcript_class

Sashimi¶

v1.11.0+ viz_kind: sashimi

Splice junctions as arcs over a region, weighted by read support, with coverage and an exon model underneath.

Input: one row per junction and sample.

Column	Config key	Need	Type	Example
`chrom`	`chr_col`	required	String	`chr17`
`start`	`start_col`	required	Numeric	`7670715`
`end`	`end_col`	required	Numeric	`7673534`
`count`	`count_col`	required	Numeric	`412`, `23`
`sample`	`sample_col`	optional	String	`WT_REP1`
`annotation`	`annotation_col`	optional	String	`known`, `novel`

Coverage (coverage_dc_tag, optional), one row per bin:

Column	Config key	Need	Type	Example
`chrom`	`coverage_chr_col`	required	String	`chr17`
`start`	`coverage_position_col`	required	Numeric	`7670700`
`depth`	`coverage_value_col`	required	Numeric	`388`
`end`	`coverage_end_col`	optional	Numeric	`7670750`
`sample`	`coverage_sample_col`	optional, matches the junction `sample`	String	`WT_REP1`

Compatible inputs: STAR SJ.out.tab junctions plus binned coverage (nf-core/rnaseq, rnafusion, nanoseq).

Controls

Primary: View (Plotly, GenomeSpy), Locus
Cosmetic: Junctions kept, zoom, read depth under the arcs, log depth axis, exon support, exon model lane, arc width and colour

YAML

- tag: viz-sashimi
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: junctions
  viz_kind: sashimi
  config:
    viz_kind: sashimi
    chr_col: chrom
    start_col: start
    end_col: end
    count_col: count
    sample_col: sample
    annotation_col: annotation
    coverage_dc_tag: binned_coverage
    coverage_chr_col: chrom
    coverage_position_col: start
    coverage_end_col: end
    coverage_value_col: depth
    coverage_sample_col: sample
    views: [genomespy, plotly]

Gene arrow track¶

v1.11.0+ viz_kind: gene_arrow_track

One arrow per coding sequence along a contig, the way a gene cluster or a resistance cassette is read.

Input: one row per gene.

Column	Config key	Need	Type	Example
`contig`	`contig_col`	required	String	`NODE_12_length_84211`
`feature_id`	`feature_id_col`	required	String	`PROKKA_01234`
`start`	`start_col`	required	Numeric	`1200`
`end`	`end_col`	required	Numeric	`2850`
`strand`	`strand_col`	required	String	`+`, `-`
`gene_class`	`class_col`	optional, arrow colour	String	`biosynthetic`
`label`	`label_col`	optional, text above the arrow	String	`ermB`
`region_start`	`region_start_col`	optional, the lane window	Numeric	`1000`
`region_end`	`region_end_col`	optional, the lane window	Numeric	`25000`

Compatible inputs: antiSMASH or nf-core/funcscan BGC calls, Prokka or Bakta annotations (nf-core/mag, bacass).

Controls

Primary: Lanes shown, Lane order, Align lanes
Cosmetic: Highlight region, feature labels, arrow height

YAML

- tag: viz-gene-arrow-track
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: bgc_genes
  viz_kind: gene_arrow_track
  config:
    viz_kind: gene_arrow_track
    contig_col: contig
    feature_id_col: feature_id
    start_col: start
    end_col: end
    strand_col: strand
    class_col: gene_class
    label_col: label

Variants & rearrangements¶

Manhattan¶

v0.13.0+ viz_kind: manhattan

A score along the genome, chromosomes end to end. mode: rainfall plots the distance between variants instead, so mutation clusters sink.

Input: one row per variant.

Column	Config key	Need	Type	Example
`chr`	`chr_col`	required	String	`chr1`, `chr19`
`pos`	`pos_col`	required	Integer	`109274968`
`score`	`score_col`	required, usually -log10(p)	Float	`12.4`
`feature`	`feature_col`	optional	String	`rs12740374`
`beta`	`effect_col`	optional	Float	`0.21`

Compatible inputs: PLINK .assoc, GWAS or QTL summary statistics, somatic VCFs (nf-core/sarek).

Controls

Primary: Figure (Score, Rainfall), Colour by, Chromosomes, Threshold, Highlight
Cosmetic: Top-N labels, marker size

YAML

- tag: viz-manhattan
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: gwas_hits
  viz_kind: manhattan
  config:
    viz_kind: manhattan
    chr_col: chr
    pos_col: pos
    score_col: score
    feature_col: feature
    score_threshold: 5.0
    selection_enabled: true
    selection_column: feature

Lollipop¶

v0.13.0+ viz_kind: lollipop

Variants as stems along a gene or protein, coloured by consequence. With selection_enabled a click also picks the residue for the protein tiles.

Input: one row per variant.

Column	Config key	Need	Type	Example
`Hugo_Symbol`	`feature_id_col`	required	String	`TP53`, `KRAS`
`Protein_position`	`position_col`	required	Integer	`175`
`Variant_Classification`	`category_col`	required	String	`Missense_Mutation`
`VAF`	`effect_col`	optional	Float	`0.42`
`HGVSp_Short`	`label_col`	optional, names the stem	String	`p.R175H`

Compatible inputs: Mutation Annotation Format tables (maftools, vcf2maf) or VEP / snpEff annotated VCFs (nf-core/sarek).

Controls

Primary: Gene, Sort genes
Cosmetic: Point size, stem width, scale points by |effect|, show stems, marker outline, palette, label top-N

YAML

- tag: viz-lollipop
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: variants
  viz_kind: lollipop
  config:
    viz_kind: lollipop
    feature_id_col: Hugo_Symbol
    position_col: Protein_position
    category_col: Variant_Classification
    effect_col: VAF
    label_col: HGVSp_Short

Oncoplot¶

v0.13.0+ viz_kind: oncoplot

A sample by gene mutation matrix, cells coloured by mutation type, with frequency strips.

Input: one row per mutation (sample and gene).

Column	Config key	Need	Type	Example
`Tumor_Sample_Barcode`	`sample_id_col`	required	String	`TCGA-A1-A0SB-01`
`Hugo_Symbol`	`gene_col`	required	String	`TP53`, `PIK3CA`
`Variant_Classification`	`mutation_type_col`	required	String	`Missense_Mutation`

Compatible inputs: Mutation Annotation Format tables: Tumor_Sample_Barcode, Hugo_Symbol, Variant_Classification (nf-core/sarek).

Controls

Primary: Sort by mutation frequency
Cosmetic: None

YAML

- tag: viz-oncoplot
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: somatic_maf
  viz_kind: oncoplot
  config:
    viz_kind: oncoplot
    sample_id_col: Tumor_Sample_Barcode
    gene_col: Hugo_Symbol
    mutation_type_col: Variant_Classification

Genome chord¶

v1.13.0+ viz_kind: genome_chord

Chromosomes on a ring, one chord per link between two loci: fusions, breakends, translocations.

Input: one row per link between two loci.

Column	Config key	Need	Type	Example
`chrom_a`	`chrom_a_col`	required	String	`chr9`
`pos_a`	`pos_a_col`	required	Numeric	`130714000`
`chrom_b`	`chrom_b_col`	required	String	`chr22`
`pos_b`	`pos_b_col`	required	Numeric	`23290000`
`support`	`weight_col`	optional, link weight	Numeric	`54`
`sv_type`	`category_col`	optional, colour by	String	`BND`, `INV`
`label`	`label_col`	optional	String	`BCR::ABL1`
`sample`	`sample_col`	optional	String	`TUMOUR_A`

Compatible inputs: Manta, TIDDIT or SvABA breakends (nf-core/sarek), arriba or STAR-Fusion fusions (nf-core/rnafusion).

Controls

Primary: Assembly, Colour by
Cosmetic: Links drawn, minimum weight, intra-chromosomal links, chromosome labels

YAML

- tag: viz-genome-chord
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: sv_links
  viz_kind: genome_chord
  config:
    viz_kind: genome_chord
    chrom_a_col: chrom_a
    pos_a_col: pos_a
    chrom_b_col: chrom_b
    pos_b_col: pos_b
    weight_col: support
    category_col: sv_type
    assembly: hg38

Fusion structure¶

v1.11.0+ viz_kind: fusion_structure

A fusion drawn as its two partners, with the protein domains kept or lost at the breakpoint.

Input: one row per domain of each partner.

Column	Config key	Need	Type	Example
`fusion_id`	`fusion_id_col`	required	String	`BCR::ABL1`
`partner`	`partner_col`	required	String	`BCR`, `ABL1`
`feature`	`feature_col`	required	String	`SH3`
`start`	`start_col`	required	Numeric	`61`
`end`	`end_col`	required	Numeric	`121`
`breakpoint`	`breakpoint_col`	optional	Numeric	`426`
`retained`	`retained_col`	optional, fraction kept, 0 to 1	Numeric	`1.0`, `0.4`
`source`	`colour_by_col`	optional, domain colour	String	`Pfam`

Compatible inputs: Arriba or STAR-Fusion calls (nf-core/rnafusion).

Controls

Primary: Fusions (how many)
Cosmetic: Bar height, mark the breakpoint, name each domain, position axis

YAML

- tag: viz-fusion-structure
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: fusion_domains
  viz_kind: fusion_structure
  config:
    viz_kind: fusion_structure
    fusion_id_col: fusion_id
    partner_col: partner
    feature_col: feature
    start_col: start
    end_col: end
    breakpoint_col: breakpoint
    retained_col: retained

Signal & read profiles¶

Profile¶

v1.11.0+ viz_kind: profile

One curve per series over an ordered numeric axis, with an optional band. A TSS profile, a fragment-length ladder or a per-residue pLDDT curve.

Input: one row per series and x value (long format).

Column	Config key	Need	Type	Example
`sample`	`series_col`	required	String	`H3K4me3_rep1`
`distance`	`x_col`	required	Numeric	`-1000`, `0`
`signal`	`y_col`	required	Numeric	`6.41`
`lower`	`lower_col`	optional, the band	Float	`5.90`
`upper`	`upper_col`	optional, the band	Float	`6.92`

Compatible inputs: deepTools profiles (nf-core/atacseq, chipseq), riboWaltz, crisprseq.

Controls

Primary: Log x, Log y, Local log-log slope panel
Cosmetic: Line width, band opacity, legend

YAML

- tag: viz-profile
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: tss_profile
  viz_kind: profile
  config:
    viz_kind: profile
    series_col: sample
    x_col: distance
    y_col: signal
    reference_x: 0
    reference_label: TSS

Signal matrix¶

v1.11.0+ viz_kind: signal_matrix

The heatmap under a profile: one row per region, one column per offset, rows ordered by signal.

Input: one row per region and offset (long format).

Column	Config key	Need	Type	Example
`region_id`	`region_id_col`	required	String	`peak_00412`
`position`	`position_col`	required	Numeric	`-500`, `0`
`value`	`value_col`	required	Numeric	`8.7`
`group`	`group_col`	optional	String	`H3K27ac`

Compatible inputs: deepTools computeMatrix output in long form (nf-core/atacseq, chipseq, cutandrun).

Controls

Primary: Row order, Max rows
Cosmetic: Colour scale, mean profile above the matrix

YAML

- tag: viz-signal-matrix
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: peak_matrix
  viz_kind: signal_matrix
  config:
    viz_kind: signal_matrix
    region_id_col: region_id
    position_col: position
    value_col: value
    group_col: group
    reference_label: Peak summit

Damage profile¶

v1.13.0+ viz_kind: damage_profile

Ancient-DNA misincorporation by distance from the read end. C>T at 5' and G>A at 3' are highlighted.

Input: one row per sample, read end, position and substitution.

Column	Config key	Need	Type	Example
`sample`	`sample_col`	required	String	`Lib_01`
`end`	`end_col`	required	String	`5p`, `3p`
`position`	`position_col`	required	Numeric	`1`
`base_change`	`base_change_col`	required	String	`C>T`, `G>A`
`frequency`	`frequency_col`	required	Numeric	`0.231`
`length_bin`	`length_bin_col`	optional, one lane per bin with `facet_by: length_bin`	String	`30-49`

Compatible inputs: DamageProfiler or mapDamage substitution tables (nf-core/eager).

Controls

Primary: Ends, Highlight, One lane per read-length bin
Cosmetic: Max position

YAML

- tag: viz-damage-profile
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: misincorporation
  viz_kind: damage_profile
  config:
    viz_kind: damage_profile
    sample_col: sample
    end_col: end
    position_col: position
    base_change_col: base_change
    frequency_col: frequency

Microbiome & ecology¶

Stacked taxonomy¶

v0.13.0+ viz_kind: stacked_taxonomy

Per-sample composition at one taxonomic rank, the tail folded into Other, with optional metadata strips.

Input: one row per sample, taxon and rank (long format).

Column	Config key	Need	Type	Example
`sample_id`	`sample_id_col`	required	String	`S01`
`taxon`	`taxon_col`	required	String	`Bacteroidota`
`rank`	`rank_col`	required	String	`Phylum`, `Genus`
`abundance`	`abundance_col`	required	Numeric	`0.42`

Compatible inputs: QIIME2 taxa-collapse tables (nf-core/ampliseq), taxprofiler or mag abundance tables.

Controls

Primary: Rank, Top-N taxa, Sort samples, Normalise
Cosmetic: Legend, log y

YAML

- tag: viz-stacked-taxonomy
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: taxa_long
  viz_kind: stacked_taxonomy
  config:
    viz_kind: stacked_taxonomy
    sample_id_col: sample_id
    taxon_col: taxon
    rank_col: rank
    abundance_col: abundance
    default_rank: Phylum
    top_n: 12

Sunburst¶

v0.13.0+ viz_kind: sunburst

A taxonomy or pathway hierarchy as rings from root to leaf, each ring a shade of its lineage.

Input: one row per leaf, one column per rank (wide format), root first.

Column	Config key	Need	Type	Example
`Kingdom`, `Phylum`, `Class`, `Order`, `Family`, `Genus`	`rank_cols`	required, root first	String	`Bacteria`, `Bacteroides`
`abundance`	`abundance_col`	required	Numeric	`1520`

Compatible inputs: Kraken2 .kreport pivoted to rank columns, nf-core/ampliseq or taxprofiler classifications.

Controls

Primary: Start from rank, Max depth, Colour by rank
Cosmetic: Palette, min arc (% of root), show % on arcs

YAML

- tag: viz-sunburst
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: taxa_wide
  viz_kind: sunburst
  config:
    viz_kind: sunburst
    rank_cols: [Kingdom, Phylum, Class, Order, Family, Genus]
    abundance_col: abundance

Rarefaction¶

v0.13.0+ viz_kind: rarefaction

Alpha diversity against sequencing depth, one curve per sample, mean and SE over iterations.

Input: one row per sample, depth and iteration, one column per metric.

Column	Config key	Need	Type	Example
`sample_id`	`sample_id_col`	required	String	`S01`
`depth`	`depth_col`	required	Numeric	`1000`
`shannon`	`metric_col`	required, the metric shown first	Numeric	`3.82`
`observed_features`, `faith_pd`	`metric_options`	optional, the metric tabs	Numeric	`212`
`iter`	`iter_col`	optional	Numeric	`1`, `2`
`habitat`	`group_col`	optional, group by	String	`soil`, `marine`

Compatible inputs: QIIME2 alpha-rarefaction tables (nf-core/ampliseq).

Controls

Primary: Metric tabs, Group by, Top-N samples
Cosmetic: Error bars (±SE)

YAML

- tag: viz-rarefaction
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: rarefaction_long
  viz_kind: rarefaction
  config:
    viz_kind: rarefaction
    sample_id_col: sample_id
    depth_col: depth
    metric_col: shannon
    metric_options: [shannon, observed_features, faith_pd]
    iter_col: iter
    group_col: habitat

Phylogenetic tree¶

v0.13.0+ viz_kind: phylogenetic

A Newick tree with tip metadata, five layouts, clade selection, filter and collapse. collapse_rank turns it into a summary by rank.

Summary by rank (View: Summary by rank, Collapse to: Genus, Top N: 12):

Input: two data collections, joined on the tree's tip labels, plus an optional third.

Collection	DC type	Config key	Content
Tree	`phylogeny`, a special DC: the Newick or Nexus file is read as is, never turned into a table	`tree_dc_tag`	one tree, tips labelled `ASV_0001`, `ASV_0002`...
Tip metadata	`table`	`metadata_dc_tag` (the tile's `data_collection_tag`)	one row per tip, columns below
Abundance, optional	`table`	`abundance_dc_tag`	one row per tip and sample, sizes the summary by reads

The project declares the phylogeny DC with a link to its metadata table, see Phylogeny DCs and their metadata table.

Tip metadata columns:

Column	Config key	Need	Type	Example
`taxon`	`taxon_col`	required, matches the tree's tip labels	String	`ASV_0001`
`Phylum`	`color_col`	optional, tip colour	Numeric or String	`Bacteroidota`
`Genus`	`label_col`	optional, shown beside the tip label	String	`Bacteroides`
`Class`, `Order`	`extra_color_cols`	optional, more Colour by choices	String	`Bacteroidia`

Abundance table columns are bound by abundance_col and abundance_sample_col.

Compatible inputs: IQ-TREE or FastTree Newick plus a tip metadata table (nf-core/bactmap, pathogensurveillance, ampliseq).

Controls

Primary: View (Full tree, Summary by rank), Colour by, Search tip, Layout, Ladderise; summary: Collapse to, Top N
Cosmetic: Label by, metadata strips, legend, support values, scale bar; toolbar: undo, redo, zoom and pan, reset, focus mode

YAML

- tag: viz-phylogenetic
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: tree_metadata
  viz_kind: phylogenetic
  config:
    viz_kind: phylogenetic
    tree_wf_id: 646b0f3c1e4a2d7f8e5b8ca3   # placeholder ids, rewritten
    tree_dc_id: 646b0f3c1e4a2d7f8e5b8cdb   # from tree_dc_tag at import
    tree_dc_tag: phylogenetic_tree
    metadata_dc_tag: tree_metadata
    taxon_col: taxon
    color_col: Phylum

Samples & specimens¶

Allele grid¶

v1.20.0+ viz_kind: allele_grid

A sample by locus grid of diploid genotypes (HLA typing). Each cell is split into its two haplotypes and coloured by allele, one hue family per allele group, and a homozygous locus is one merged cell. With selection_enabled, a click on an allele filters the dashboard to the rows carrying it.

Input: one row per allele call (sample, locus, haplotype), melted long.

Column	Config key	Need	Type	Example
`sample_id`	`sample_id_col`	required	String	`SAMPLE_BAM`
`locus`	`locus_col`	required	String	`HLA-A`, `HLA-B`
`allele`	`allele_col`	required	String	`HLA-A*02:01`
`haplotype`	`haplotype_col`	optional, 1 or 2; else table order	Integer	`1`
`hla_class`	`category_col`	optional, groups the loci under a header	String	`Class I`
`objective`	`value_col`	optional, side bar	Numeric	`1108.68`
`reads`	`reads_col`	optional, side bar or cell opacity	Numeric	`1129`

Compatible inputs: OptiType genotypes (nf-core/hlatyping), reshaped to one row per call; LILAC and arcasHLA calls as they are written.

Controls

Primary: Resolution, Order samples (and the Locus to order by)
Cosmetic: Allele labels, fade cells by read support, side bars

YAML

- tag: viz-allele-grid
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: hla_genotypes
  viz_kind: allele_grid
  config:
    viz_kind: allele_grid
    sample_id_col: sample_id
    locus_col: locus
    allele_col: allele
    haplotype_col: haplotype
    category_col: hla_class
    value_col: objective
    reads_col: reads
    resolution: 2
    selection_enabled: true
    selection_column: allele

Pedigree¶

v1.20.0+ viz_kind: pedigree

A family tree from a PED-style table: generations top to bottom, couple and sibship lines, a square, circle or diamond by sex, filled when affected. With selection_enabled, a click on an individual filters the dashboard to it.

Input: one row per individual. Parents are 0, empty or null for a founder; sex is 1 / 2 / 0 or a word, status 2 / 1 / 0 or a word.

Column	Config key	Need	Type	Example
`individual`	`individual_col`	required	String or Integer	`F1_I1`
`father`	`father_col`	required	String or Integer	`0`, `F1_I1`
`mother`	`mother_col`	required	String or Integer	`0`, `F1_I2`
`sex`	`sex_col`	required	Numeric or String	`1`, `female`
`status`	`status_col`	required, affected status	Numeric or String	`2`, `unaffected`
`family`	`family_col`	optional, one tree per value	String or Integer	`FAM001`
`label`	`label_col`	optional, text under each symbol	String	`I-1`, `Proband`
`deceased`	`deceased_col`	optional, diagonal slash	Boolean or String	`1`
`proband`	`proband_col`	optional, arrow; else the first affected child	Boolean or String	`proband`

Compatible inputs: A PED or samplesheet table with family, sample, father, mother, sex and phenotype columns, such as the one nf-core/raredisease reads.

Controls

Primary: Family, Families with an affected member only, Max families, Max individuals
Cosmetic: Labels under symbols, label text, symbol size, generation spacing, generation numerals, family names, colour affected by, legend

YAML

- tag: viz-pedigree
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: samples
  viz_kind: pedigree
  config:
    viz_kind: pedigree
    individual_col: individual
    father_col: father
    mother_col: mother
    sex_col: sex
    status_col: status
    family_col: family
    label_col: label
    selection_enabled: true
    selection_column: individual

Ideogram¶

v1.20.0+ viz_kind: ideogram

A karyotype: one bar per chromosome scaled to its length, with a glyph per feature or density bins on it, one karyotype per genome or sample. Click a chromosome to open it with its own bins, a bp axis and zoom; from there the dashboard can be filtered to the chromosome or the visible range.

Input: one row per feature or window, on a chromosome.

Column	Config key	Need	Type	Example
`chrom`	`chrom_col`	required	String	`chr1`, `X`
`start`	`start_col`	required	Numeric	`1000000`
`end`	`end_col`	required	Numeric	`2000000`
`value`	`value_col`	optional, density on a colour scale	Numeric	`12.4`
`svtype`	`category_col`	optional, categorical colour	String	`DEL`, `complete`
`sample`	`sample_col`	optional, one karyotype per value	String	`NA12878_75M`
`label`	`label_col`	optional, hover name	String	`DEL`
`sequence_length`	`chrom_length_col`	optional, else `assembly`, else the last feature	Numeric	`248956422`

Compatible inputs: Structural variants from nf-core/sarek, BUSCO placements and telomeric repeats from nf-core/genomeqc, variant density per window from a VCF.

Controls

Primary: Genome, Go to chromosome, Draw features as (Auto, Marks, Density)
Cosmetic: Assembly, Bars (rows or columns), Colour (category or value), bin size, colour scale, feature opacity

YAML

- tag: viz-ideogram
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: sv_calls
  viz_kind: ideogram
  config:
    viz_kind: ideogram
    chrom_col: chrom
    start_col: pos
    end_col: end
    category_col: svtype
    sample_col: sample
    label_col: svtype
    assembly: hg38
    mode: auto
    orientation: horizontal

Spatial cells¶

v1.20.0+ viz_kind: spatial_cells

Segmented cells where they sit in the image: one marker per cell at its centroid, sized by its area, coloured by a marker picked in the panel or by cell type, optionally over an image of the sample. A lasso selects cells.

Input: one row per segmented cell, wide: one intensity column per marker.

Column	Config key	Need	Type	Example
`cell_key`	`cell_id_col`	required, unique across samples	String or Integer	`TEST1\\|Cellpose\\|1`
`X_centroid`	`x_col`	required	Numeric	`395.4`
`Y_centroid`	`y_col`	required, grows downwards	Numeric	`16.8`
`DNA_6`, `CD45`, ...	`value_columns` or `value_columns_pattern`	optional, the markers to pick from	Numeric	`14242.9`
`segmenter`	`category_col`	optional, categorical colour	String	`Cellpose`
`sample`	`sample_col`	optional, one image each	String	`TEST1`
`Area`	`area_col`	optional, sizes the marker	Numeric	`180`

Compatible inputs: MCQUANT cell tables.

Controls

Primary: Marker, Colour (marker or category), Sample, Transform (Linear, asinh, log1p)
Cosmetic: Clip low and high, asinh cofactor, colour scale, reverse scale, size by area, size, opacity, Y axis, Samples (one or side by side), image underlay and opacity, legend, hover columns

YAML

- tag: viz-spatial-cells
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: mcquant_cells
  viz_kind: spatial_cells
  config:
    viz_kind: spatial_cells
    cell_id_col: cell_key
    x_col: X_centroid
    y_col: Y_centroid
    category_col: segmenter
    sample_col: sample
    area_col: Area
    value_columns: [DNA_6, CD45, CD57]
    color_by: value
    transform: asinh
    selection_enabled: true
    selection_column: cell_key

General purpose¶

Scatter (X/Y)¶

v1.11.0+ viz_kind: scatter_xy

Numeric against numeric, with a size column, a reference line, log axes and a selection key.

Input: one row per point.

Column	Config key	Need	Type	Example
`rep_a`	`x_col`	required	Numeric	`812.4`, `15.2`
`rep_b`	`y_col`	required	Numeric	`790.1`, `22.8`
`gene`	`label_col`	optional, hover and selection label	String	`GAPDH`
`mean_expression`	`size_col`	optional, marker size	Numeric	`801.3`
`biotype`	`color_col`	optional, marker colour	String	`protein_coding`

Compatible inputs: Any table with two numeric columns: replicate concordance, QC metric pairs.

Controls

Primary: Cloud (Points, Density), Log x, Log y, Reference line, Reference value, Highlight
Cosmetic: Marker size, opacity, marker outline, top-N labels, colourscale, legend

YAML

- tag: viz-scatter-xy
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: normalised_counts
  viz_kind: scatter_xy
  config:
    viz_kind: scatter_xy
    x_col: rep_a
    y_col: rep_b
    label_col: gene
    size_col: mean_expression
    reference_line: diagonal
    log_x: true
    log_y: true

Hierarchical heatmap¶

v0.13.0+ viz_kind: complex_heatmap

A clustered matrix with dendrograms and annotation tracks, computed on the server.

Input: one row per sample, one numeric column per gene (wide format).

Column	Config key	Need	Type	Example
`sample_id`	`index_column`	required	String	`ctrl_1`, `treat_1`
`TP53`, `EGFR`, ...	`value_columns`	required, every numeric column when unset	Numeric	`9.81`, `7.42`
`condition`	`row_annotation_cols`	optional, annotation strip	String	`control`, `treated`

Compatible inputs: A normalised count matrix such as DESeq2 vst() (nf-core/rnaseq, differentialabundance).

Controls

Primary: Normalisation, Clustering method, Cluster rows, Cluster columns
Cosmetic: Row annotations, column annotations

Height v1.19.3+: max_rows (3 to 16) lets the tile grow to fit a large matrix, up to that many grid rows; unset, it keeps its layout height and only shrinks for a small matrix. min_cell_px (2 to 40, 12 when unset) is the shortest row height the tile asks the grid for.

YAML

- tag: viz-complex-heatmap
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: vst_matrix
  viz_kind: complex_heatmap
  config:
    viz_kind: complex_heatmap
    index_column: sample_id
    row_annotation_cols: [condition]
    normalize: row_z
    cluster_method: ward

UpSet¶

v0.13.0+ viz_kind: upset_plot

Set intersections as bars over a dot matrix: the readable alternative to a Venn diagram.

Input: one row per item, one 0/1 column per set.

Column	Config key	Need	Type	Example
`contrastA`, `contrastB`, `contrastC`	`set_columns`	required, the 0/1 columns when unset	Integer (0/1)	`1`, `0`

Compatible inputs: Any binary membership table: features called per contrast, taxa per site.

Controls

Primary: Sort by, Order, Min intersection size, Colour intersections by
Cosmetic: Show annotations, set-size bars, intersection count labels, annotation tracks

YAML

- tag: viz-upset-plot
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: membership
  viz_kind: upset_plot
  config:
    viz_kind: upset_plot
    set_columns: [contrastA, contrastB, contrastC]
    sort_by: cardinality
    min_size: 1

Sankey¶

v0.13.0+ viz_kind: sankey

Categorical flow across ordered levels, such as sample to lineage to clade.

Input: one row per item, one categorical column per level, in order.

Column	Config key	Need	Type	Example
`qc_status`, `lineage`, `clade`	`step_cols`	required, 2 or more, in order	String	`pass`, `XBB.1.5`
`count`	`value_col`	optional, link weight; unset counts rows	Numeric	`12`

Compatible inputs: Any tidy table with ordered categorical columns (nf-core/viralrecon QC, Pangolin and Nextclade).

Controls

Primary: Depth, Colour links by, Sort nodes
Cosmetic: Link opacity, node labels, min link value

YAML

- tag: viz-sankey
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: lineage_calls
  viz_kind: sankey
  config:
    viz_kind: sankey
    step_cols: [qc_status, lineage, clade]

Parallel coordinates¶

v1.13.0+ viz_kind: parallel_coordinates

One polyline per sample across many metric axes. A brush on an axis becomes a range filter.

Input: one row per sample.

Column	Config key	Need	Type	Example
`sample`	`sample_col`	required	String	`WT_REP1`
`total_reads`, `percent_duplicates`, `percent_gc`, `percent_aligned`	`metric_cols`	required, every numeric column when unset	Numeric	`24813402`, `18.2`
`group`	`group_col`	optional, line colour	String	`WT`, `KO`

Compatible inputs: Any per-sample QC table, such as MultiQC general statistics.

Controls

Primary: Axis scale, Colour by, Reset brushes
Cosmetic: Colourscale, line opacity

YAML

- tag: viz-parallel-coordinates
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: qc_metrics
  viz_kind: parallel_coordinates
  config:
    viz_kind: parallel_coordinates
    sample_col: sample
    group_col: group
    metric_cols: [total_reads, percent_duplicates, percent_gc, percent_aligned]

Record card¶

v1.13.0+ viz_kind: record_card

One row of a collection as labelled fields and links, following a selection made in another tile.

Input: one row per record.

Column	Config key	Need	Type	Example
`feature_id`	`id_col`	required, matched against the selection	String	`ENSG00000141510`
`gene_symbol`	`title_col`	optional, card heading	String	`TP53`

Every other column (biotype, chromosome, start, end) is a field; sections groups them, link_templates turns one into a link.

Compatible inputs: Any table with an identifier column.

Controls

Primary: Record picker (when a selection holds several records)
Cosmetic: Fields per card

YAML

- tag: viz-record-card
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: gene_summary
  viz_kind: record_card
  config:
    viz_kind: record_card
    id_col: feature_id
    title_col: gene_symbol
    linked_component: viz-scatter-xy
    sections:
      Identity: [gene_symbol, biotype]
      Location: [chromosome, start, end]
    link_templates:
      feature_id: "https://www.ensembl.org/id/{value}"

Ranked table¶

v1.20.0+ viz_kind: ranked_table

A leaderboard of candidates ordered by a score: medals on the first three, badges coloured by value and bars in the cells, the fields behind a row in a hover popover. With selection_enabled, a click on a row filters the dashboard to it.

Input: one row per candidate (a variant, a gene). Every other column is named in the config (columns, popover_columns), not bound as a role.

Column	Config key	Need	Type	Example
`gene`	`title_col`	required, bold row name	String or Integer	`TPTE`
`rank_score`	`score_col`	required, orders the rows	Numeric	`14`
`hgvs_p`	`subtitle_col`	optional, monospace beside the title	String	`p.Arg229Ter`
`rank`	`rank_col`	optional, shown in the medal	Numeric	`1`

Compatible inputs: Ranked variants (nf-core/raredisease), outlier genes (nf-core/drop), somatic variants by priority (nf-core/sarek).

Controls

Primary: Top N, Min score, Filter by, Sort by, First (highest or lowest)
Cosmetic: Hide columns, Medals, Compact rows, Open family details

columns sets how each cell is drawn: text, mono, badge, bar or number. family_dc_tag adds a pedigree of the family to the pinned popover, see Pedigree.

YAML

- tag: viz-ranked-table
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: ranked_variants
  viz_kind: ranked_table
  config:
    viz_kind: ranked_table
    title_col: gene
    subtitle_col: hgvs_p
    score_col: rank_score
    columns:
      - {column: impact, label: Impact, display: badge}
      - {column: rank_score, label: Rank score, display: bar, decimals: 0}
    popover_columns: [consequence, gnomad_af, cadd]
    top_n: 8
    selection_enabled: true
    selection_column: variant_key

Ranked distribution¶

v1.20.0+ viz_kind: ranked_distribution

The top-N features ranked by a score, each with its distribution across samples as a box or violin beside a lollipop of the score, on one shared feature axis. Used for gene stability and housekeeping-gene panels.

Input: one row per feature, with box statistics (pre-aggregated, boxes only), or one row per feature and sample (long form, boxes or violins). Bind one shape, not both.

Column	Config key	Need	Type	Example
`gene_id`	`feature_id_col`	required	String	`ENSG00000198804`
`stability_score`	`score_col`	required, ranks the features	Numeric	`0.83`
`section_rank`	`rank_col`	optional, else ranked by the score	Numeric	`1`
`gene_name`	`label_col`	optional, axis label	String	`MT-CO1`
`section`	`group_col`	optional, colour	String	`Section 01`
`value`	`value_col`	long form	Numeric	`0.9994`
`q1`, `median`, `q3`	`q1_col`, `median_col`, `q3_col`	pre-aggregated, all three together	Numeric	`0.9996`, `0.9998`, `0.9999`
`lower`, `upper`, `mean`	`lower_col`, `upper_col`, `mean_col`	optional, pre-aggregated	Numeric	`0.999`, `1.0`

Compatible inputs: Gene stability ranking and per-sample values from nf-core/stableexpression.

Controls

Primary: Top N, Draw (Box, Violin; long form only), First (lowest or highest)
Cosmetic: Features (rows or columns), log value axis

YAML

- tag: viz-ranked-distribution
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: stable_gene_distribution
  viz_kind: ranked_distribution
  config:
    viz_kind: ranked_distribution
    feature_id_col: gene_id
    score_col: stability_score
    rank_col: section_rank
    label_col: gene_name
    group_col: section
    q1_col: q1
    median_col: median
    q3_col: q3
    top_n: 10
    ascending: true
    distribution: box
    selection_enabled: true

Benchmarking¶

PR benchmark¶

v1.10.0+ viz_kind: pr_benchmark

Each callset at its precision and recall, with F1 contours. The roc view sweeps a threshold into curves.

Input: one row per callset.

Column	Config key	Need	Type	Example
`tool`	`label_col`	required	String	`DeepVariant`
`recall`	`recall_col`	required	Float	`0.9962`
`precision`	`precision_col`	required	Float	`0.9978`
`f1`	`f1_col`	required	Float	`0.9970`
`tp`	`support_col`	optional, point size	Numeric	`3891204`
`variant_type`	`category_col`	optional	String	`SNP`, `INDEL`
`threshold`	`threshold_col`	optional, the `roc` and `both` views (one row per callset and threshold)	Numeric	`0.5`
`fpr`	`fpr_col`	optional, ROC x axis	Float	`0.002`
`sample`	`group_col`	optional, one curve per group	String	`HG002`

Compatible inputs: hap.py or RTG vcfeval summaries (nf-core/variantbenchmarking, sarek).

Controls

Primary: View (PR, ROC, both), Size, Colour scale
Cosmetic: F1 iso-contours, y = x diagonal, fixed 0-1 axes, marker size, colour bar, point labels; curves: legend, markers, shade area, show AUC

YAML

- tag: viz-pr-benchmark
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: benchmark_summary
  viz_kind: pr_benchmark
  config:
    viz_kind: pr_benchmark
    label_col: tool
    recall_col: recall
    precision_col: precision
    f1_col: f1
    support_col: tp

Confusion matrix¶

v1.10.0+ viz_kind: confusion_matrix

True positives, false positives and false negatives per callset as a heatmap.

Input: one row per callset.

Column	Config key	Need	Type	Example
`tool`	`label_col`	required	String	`DeepVariant`
`tp`	`tp_col`	required	Numeric	`3891204`
`fp`	`fp_col`	required	Numeric	`8592`
`fn`	`fn_col`	required	Numeric	`14810`
`tn`	`tn_col`	optional	Numeric	`120533`

Compatible inputs: Benchmark counts as nf-core/variantbenchmarking reports them.

Controls

Primary: Normalise
Cosmetic: Colour scale, colour bar, show fractions, font size

YAML

- tag: viz-confusion-matrix
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: benchmark_summary
  viz_kind: confusion_matrix
  config:
    viz_kind: confusion_matrix
    label_col: tool
    tp_col: tp
    fp_col: fp
    fn_col: fn

Metric with CI¶

v1.10.0+ viz_kind: metric_ci_bars

One metric per callset with its 95% confidence interval, as a forest plot.

Input: one row per callset.

Column	Config key	Need	Type	Example
`tool`	`label_col`	required	String	`DeepVariant`
`precision`	`value_col`	required	Float	`0.9978`
`precision_lower`	`lower_col`	required	Float	`0.9976`
`precision_upper`	`upper_col`	required	Float	`0.9980`

Compatible inputs: Precision or recall intervals from hap.py, som.py or vcfeval counts (nf-core/variantbenchmarking).

Controls

Primary: Sort by value
Cosmetic: Value labels, colour scale, point size

YAML

- tag: viz-metric-ci-bars
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: benchmark_summary
  viz_kind: metric_ci_bars
  config:
    viz_kind: metric_ci_bars
    label_col: tool
    value_col: precision
    lower_col: precision_lower
    upper_col: precision_upper
    metric_name: Precision

Proteins¶

Structure prediction, protein annotation and protein family runs publish a model, the alignment behind it and per-residue facts. Eight kinds draw them and stay linked by residue. The tables they read, the structure resolver and the numbering check are on the Proteins page. The nf-core proteinfold, proteinannotator and proteinfamilies templates are built on them.

3D structure¶

v1.19.0+ viz_kind: molecule_3d

The model in 3Dmol.js, coloured by confidence, chain or a value, variants as spheres. A click picks a residue, shift-click a range.

Input: one PDB or mmCIF file per protein (structure_dc_tag, pLDDT in the B-factor column), plus a residue table, one row per residue.

Column	Config key	Need	Type	Example
`position`	`position_col`	required	Numeric	`175`, `858`
`entity`	`entity_col`	optional, the protein of the row	String	`P04637`
`chain`	`chain_col`	optional	String	`A`
`conservation`	`value_col`	optional, `color_mode: value`	Numeric	`0.82`
`domain`	`category_col`	optional, `color_mode: category`	String	`DNA-binding`
`ref_aa`	`ref_aa_col`	optional, variant spheres	String	`R`
`alt_aa`	`alt_aa_col`	optional, variant spheres	String	`H`
`label`	`label_col`	optional	String	`p.R175H`
`uniprot`	`uniprot_col`	optional, `structure_source: resolve`, no file needed	String	`P04637`
`gene`	`gene_col`	optional, `structure_source: resolve`	String	`TP53`
`sequence`	`sequence_col`	optional, `structure_source: resolve` (ESMFold)	String	`MEEPQSDPSV`

See The data.

Compatible inputs: AlphaFold, ColabFold or ESMFold PDB / mmCIF (nf-core/proteinfold), or a model from AlphaFold DB.

Controls

Primary: Protein, Colour by, Style, Layout (structure alone, with sequence, alignment or text)
Cosmetic: Colour scale, variants, labels, follow selection, spin

YAML

- tag: viz-molecule-3d
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: residues
  viz_kind: molecule_3d
  config:
    viz_kind: molecule_3d
    structure_dc_tag: structures
    entity_col: entity
    position_col: position
    color_mode: plddt
    layout: structure_sequence
    selection_enabled: true

Floating structure¶

v1.19.1+ placement: floating

The 3D tile leaves the grid and floats over every tab, as a card you drag, resize, fold or dock. Only molecule_3d floats.

placement: floating             # grid (default) or floating
floating_initial_state: compact # compact, expanded, docked or hidden

Alignment¶

v1.19.0+ viz_kind: msa

A multiple sequence alignment with consensus and conservation rows. A row click selects a sequence, a column brush picks residues.

Input: one row per aligned sequence; rows of one msa_id have the same length.

Column	Config key	Need	Type	Example
`msa_id`	`msa_id_col`	required	String	`P04637`
`seq_id`	`seq_id_col`	required	String	`query`, `UniRef90_P02340`
`aligned_sequence`	`sequence_col`	required	String	`MEEPQSDLSVEPPLSQETFS-LWKLL`
`rank`	`rank_col`	optional, 0 is the query	Numeric	`0`, `1`
`identity`	`identity_col`	optional	Numeric	`0.92`

Compatible inputs: proteinfold MSAs, A3M, Stockholm or aligned FASTA.

Controls

Primary: Alignment, Colour scheme, Sort rows
Cosmetic: Column width, consensus row, conservation bars, max rows

YAML

- tag: viz-msa
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: alignments
  viz_kind: msa
  config:
    viz_kind: msa
    msa_id_col: msa_id
    seq_id_col: seq_id
    sequence_col: aligned_sequence
    rank_col: rank
    selection_enabled: true

Sequence track¶

v1.19.0+ viz_kind: sequence_track

The sequence on a ruler with a value lane, secondary structure, domains and variants. One strip per chain on a complex.

Input: a residue table, one row per residue.

Column	Config key	Need	Type	Example
`position`	`position_col`	required	Numeric	`1`, `2`
`entity`	`entity_col`	optional	String	`P04637`
`residue`	`residue_col`	optional, the letters	String	`M`, `E`
`plddt`	`value_col`	optional, the value lane	Numeric	`41.2`
`region`	`category_col`	optional	String	`disordered`

A domains table (domains_dc_tag: start, end, label) and a variants table (variants_dc_tag: position, label, category) add their lanes, as in The data.

Compatible inputs: Per-residue tables built from a structure (pLDDT), S4PRED or domain hits.

Controls

Primary: Entity, Chain
Cosmetic: Residue width, letters, value colours

YAML

- tag: viz-sequence-track
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: residues
  viz_kind: sequence_track
  config:
    viz_kind: sequence_track
    entity_col: entity
    position_col: position
    residue_col: residue
    value_col: plddt
    value_label: pLDDT
    domains_dc_tag: domains
    selection_enabled: true

HMM logo¶

v1.19.0+ viz_kind: hmm_logo

The logo of a profile HMM with insert and occupancy lanes, and where hmmsearch hits land on it. profile_source: msa computes it from an alignment instead.

Input: one row per match state and letter (long format).

Column	Config key	Need	Type	Example
`hmm_position`	`state_col`	required	Numeric	`1`, `2`
`hmm_letter`	`letter_col`	required	String	`A`, `C`
`emission`	`emission_col`	required	Float	`0.031`
`hmm_name`	`model_col`	optional, one logo per model	String	`Pkinase`
`entity`	`entity_col`	optional	String	`P00533`
`position`	`position_col`	optional, residue on the reference	Numeric	`712`
`insert_prob`	`insert_prob_col`	optional, read when present	Float	`0.02`
`insert_length`	`insert_length_col`	optional, read when present	Float	`1.4`
`occupancy`	`occupancy_col`	optional, read when present	Float	`0.98`
`consensus`	`consensus_col`	optional, read when present	String	`l`
`rf`	`rf_col`	optional, read when present	String	`x`
`cs`	`cs_col`	optional, read when present	String	`E`

The hits (hits_dc_tag) are a domain hit table with hmm_from and hmm_to. profile_source: msa reads an alignment table instead.

Compatible inputs: HMMER hmmbuild profiles and hmmsearch domain tables (hits_dc_tag), nf-core/proteinfamilies.

Controls

Primary: Heights, Colour scheme
Cosmetic: State width, consensus and insert rows, shown tracks, state window, fold below (bits), hits E-value, max hits

YAML

- tag: viz-hmm-logo
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: hmm_profile
  viz_kind: hmm_logo
  config:
    viz_kind: hmm_logo
    state_col: hmm_position
    letter_col: hmm_letter
    emission_col: emission
    model_col: hmm_name
    hits_dc_tag: domain_hits

Domain architecture¶

v1.19.0+ viz_kind: domain_architecture

The domains of many proteins, one row each, or grouped by architecture. A partial match has a zigzag edge.

Input: one row per domain hit.

Column	Config key	Need	Type	Example
`entity`	`entity_col`	required	String	`P00533`
`start`	`start_col`	required	Numeric	`712`
`end`	`end_col`	required	Numeric	`968`
`label`	`label_col`	required	String	`Pkinase_Tyr`
`protein_length`	`protein_length_col`	optional, backbone to scale	Numeric	`1210`
`hmm_from`	`hmm_from_col`	optional, partial-match edge	Numeric	`1`
`hmm_to`	`hmm_to_col`	optional, partial-match edge	Numeric	`259`
`hmm_length`	`hmm_length_col`	optional	Numeric	`259`
`hmm_coverage`	`hmm_coverage_col`	optional	Float	`0.96`
`i_evalue`	`evalue_col`	optional, tooltip	Float	`3.1e-45`
`source`	`source_col`	optional, `color_by: source`	String	`Pfam`
`description`	`description_col`	optional, tooltip	String	`Protein tyrosine kinase`
`accession`	`accession_col`	optional	String	`PF07714`

Every optional column is read when present.

Compatible inputs: InterProScan or hmmsearch domain hits (nf-core/proteinannotator, proteinfamilies).

Controls

Primary: View (Proteins, Architectures), Colour by
Cosmetic: Sources, scale, residue width, architectures, max proteins

YAML

- tag: viz-domain-architecture
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: domain_hits
  viz_kind: domain_architecture
  config:
    viz_kind: domain_architecture
    entity_col: entity
    start_col: start
    end_col: end
    label_col: label
    protein_length_col: protein_length
    view: proteins

Secondary structure¶

v1.19.0+ viz_kind: secondary_structure

Helices, strands and coil as a ribbon, with the probabilities behind the call and the agreement between sources.

Input: one row per residue, and per source when several are compared.

Column	Config key	Need	Type	Example
`position`	`position_col`	required	Numeric	`110`, `111`
`ss_code`	`state_col`	required, a DSSP or S4PRED code	String	`C`, `E`
`entity`	`entity_col`	optional	String	`P04637`
`ss_source`	`source_col`	optional, one ribbon per source	String	`S4PRED`
`residue`	`residue_col`	optional	String	`S`
`p_helix`	`p_helix_col`	optional	Float	`0.08`
`p_strand`	`p_strand_col`	optional	Float	`0.83`
`p_coil`	`p_coil_col`	optional	Float	`0.13`
`confidence`	`confidence_col`	optional, ribbon shading	Float	`0.71`

Compatible inputs: S4PRED .ss2 predictions.

Controls

Primary: Entity, Reference
Cosmetic: Residue width, ribbon height, letters, confidence shading, coil segments, min segment, colours

YAML

- tag: viz-secondary-structure
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: ss_calls
  viz_kind: secondary_structure
  config:
    viz_kind: secondary_structure
    entity_col: entity
    position_col: position
    state_col: ss_code
    source_col: ss_source
    reference_source: S4PRED
    p_helix_col: p_helix
    p_strand_col: p_strand
    p_coil_col: p_coil

Predicted aligned error¶

v1.19.0+ viz_kind: pae_matrix

A model's PAE matrix with pLDDT strips. A low-error block on the diagonal is a confident domain. A brush picks the scored range.

Input: one PAE file per protein (a pae file collection, pae_dc_tag), plus a residue table, one row per residue.

Column	Config key	Need	Type	Example
`position`	`position_col`	required	Numeric	`1`, `2`
`entity`	`entity_col`	optional, picks the PAE file	String	`P04637`
`plddt`	`value_col`	optional, the pLDDT strips	Numeric	`41.2`
`chain`	`chain_col`	optional, chain boundaries	String	`A`

See The data.

Compatible inputs: proteinfold PAE TSV, AlphaFold DB or ColabFold JSON.

Controls

Primary: Entity, Colours
Cosmetic: pLDDT strips, brush (diagonal, rectangle)

YAML

- tag: viz-pae-matrix
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: residues
  viz_kind: pae_matrix
  config:
    viz_kind: pae_matrix
    pae_dc_tag: pae_files
    entity_col: entity
    position_col: position
    value_col: plddt

Ramachandran¶

v1.19.0+ viz_kind: ramachandran

Backbone phi and psi of the model, computed in the browser from the 3D tile's file. The favoured regions are a guide, not MolProbity contours.

Input: the structure file of the 3D structure tile, plus a residue table, one row per residue.

Column	Config key	Need	Type	Example
`position`	`position_col`	required	Numeric	`175`, `858`
`entity`	`entity_col`	optional	String	`P04637`
`chain`	`chain_col`	optional	String	`A`
`conservation`	`value_col`	optional, point colour	Numeric	`0.82`
`domain`	`category_col`	optional, point colour	String	`DNA-binding`
`uniprot`	`uniprot_col`	optional, `structure_source: resolve`	String	`P04637`
`gene`	`gene_col`	optional, `structure_source: resolve`	String	`TP53`
`sequence`	`sequence_col`	optional, `structure_source: resolve`	String	`MEEPQSDPSV`

Compatible inputs: The structure file the 3D tile reads.

Controls

Primary: Protein, Colour by, Residue classes
Cosmetic: Approximate favoured regions, marker size, follow selection

YAML

- tag: viz-ramachandran
  component_type: advanced_viz
  workflow_tag: my_workflow
  data_collection_tag: residues
  viz_kind: ramachandran
  config:
    viz_kind: ramachandran
    structure_dc_tag: structures
    entity_col: entity
    position_col: position
    color_mode: plddt