dendroviz 0.1.3

Generate dendrogram scaffolding CSV and SVG from rooted tree data.

DendroViz

DendroViz takes CSV, JSON, or Newick input and turns it into a dendrogram dataset. The CSV output can be used in Tableau and other charting tools. The tool can also create SVG images.

Vertical tree with straight lines

Horizontal tree with curved lines

Radial tree with split lines

Table of Contents

• Installation
• Quickstart
• Input Format
• Colour Palettes
• Release Process
• CLI Reference
• Development

Installation

pip install dendroviz

Install the optional Newick parser only if you need it:

pip install biopython

For local development:

pip install -e .[dev]

Quickstart

Python API

from dendroviz import DendrogramGenerator, LayoutOptions

generator = DendrogramGenerator()
result = generator.generate_tree(
    "examples/dummy_deep.csv",
    tree_layout="radial",
    line_style="split",
    output_csv="build/dummy-deep-radial-split.csv",
    output_json="build/dummy-deep.json",
    output_svg="build/dummy-deep-radial-split.svg",
    show_labels=True,
    options=LayoutOptions(
        label_mode="leaves",
        show_internal_nodes=True,
        show_root_node=True,
        label_orientation="auto",
        label_offset=24,
        colour_mode="palette",
        palette="set2",
        palette_depth=2,
    ),
)

print(len(result.nodes), len(result.edges))

CLI

dendroviz build examples/dummy_deep.csv \
  --input-format csv \
  --tree-layout radial \
  --line-style split \
  --output-svg build/dummy-deep-radial-split.svg \
  --show-labels \
  --label-mode leaves \
  --label-orientation auto \
  --label-offset 24 \
  --colour-mode palette \
  --palette set2 \
  --palette-depth 2 \
  --show-palette-legend

Example test runs:

dendroviz build examples/dummy_small.csv \
  --tree-layout vertical \
  --line-style straight \
  --output-csv build/dummy-small-vertical-straight.csv \
  --output-svg build/dummy-small-vertical-straight.svg \
  --show-labels \
  --colour-mode palette \
  --palette set2 \
  --palette-depth 2

dendroviz build examples/dummy_small.csv \
  --tree-layout horizontal \
  --line-style curved \
  --output-csv build/dummy-small-horizontal-curved.csv \
  --output-svg build/dummy-small-horizontal-curved.svg \
  --show-labels \
  --label-mode all \
  --label-offset 28 \
  --colour-mode palette \
  --palette set2 \
  --palette-depth 2

dendroviz build examples/dummy_deep.csv \
  --tree-layout radial \
  --line-style split \
  --output-csv build/dummy-deep-radial-split.csv \
  --output-svg build/dummy-deep-radial-split.svg \
  --show-labels \
  --label-orientation auto \
  --colour-mode palette \
  --palette set2 \
  --palette-depth 2

Try it with the included dummy data:

• dummy_small.csv
• dummy_medium.csv
• dummy_deep.csv

Input Format

CSV

The library expects a single rooted tree with exactly these columns:

id,parent,label,order
root,,Root,0
branch_a,root,Branch A,0
branch_b,root,Branch B,1
leaf_a1,branch_a,Leaf A1,0
leaf_a2,branch_a,Leaf A2,1
leaf_b1,branch_b,Leaf B1,0

Rules:

• id must be unique
• parent is empty for the single root row
• every non-root parent must exist
• order controls sibling order and must be numeric
• cycles are not allowed

JSON

JSON input uses the same row fields as CSV. The loader accepts either:

• a top-level array of node objects
• an object with a nodes array

Each node object should include:

• id
• parent
• label
• order

Example:

{
  "nodes": [
    { "id": "root", "parent": null, "label": "Root", "order": 0 },
    { "id": "left", "parent": "root", "label": "Left", "order": 0 },
    { "id": "right", "parent": "root", "label": "Right", "order": 1 }
  ]
}

Rules:

• id must be unique
• parent is null for the single root row
• every non-root parent must exist
• order controls sibling order and must be numeric
• cycles are not allowed

Newick

Newick input is also supported when BioPython is installed. Install it with pip install biopython:

from dendroviz import DendrogramGenerator

generator = DendrogramGenerator()
tree = generator.load_tree("examples/tree.nwk", input_format="newick")

Sibling order is taken from the order children appear in the Newick file.

CLI Reference

Mandatory

Option	Values	Notes
build	subcommand	Generate dendrogram artefacts from an input tree
input path	path	Path to the input tree file
--tree-layout	radial, vertical, horizontal	radial uses angle/radius coordinates, vertical grows top-to-bottom, horizontal grows left-to-right
--line-style	curved, split, straight	curved uses smooth splines, split branches at forks, straight uses direct segments
output flag(s)	--output-csv, --output-json, --output-svg	Write one or more render artefacts

Optional

These CLI flags map directly to LayoutOptions fields in the Python API.

Option	Values	Notes
--log-level	CRITICAL, ERROR, WARNING, INFO, DEBUG	Controls CLI verbosity
--show-labels	flag	Enables SVG labels
--label-mode	all, leaves, none	leaves shows labels only on leaf nodes; none hides all labels
--label-orientation	horizontal, auto	auto flips radial labels to stay readable on the left side
--label-offset	number	Pushes labels farther from the tree
--font-size	number	Controls label size
--hide-internal-nodes	flag	Hides non-leaf node markers
--hide-root-node	flag	Hides the root node marker
--colour-mode	global, palette	Controls whether palette colouring is used
--palette	preset name or hex colours	Used only when --colour-mode palette is active
--palette-depth	1, 2, ...	Used only when --colour-mode palette is active; chooses which tree level gets palette colouring
--show-palette-legend	flag	Adds a small SVG legend when palette colouring is active
--show-svg-data-attributes	flag	Adds data-* metadata to SVG nodes and edges for browser scripting
--show-svg-titles	flag	Adds short hover titles to SVG nodes and edges
--svg-title-parts	comma-separated parts	Controls node tooltip content, for example label or label,group
--svg-title-template	template string	Controls node tooltip text, for example Family: {group}\nLanguage: {label}
--node-colour	hex colour	Fallback node colour in global mode
--edge-colour	hex colour	Fallback edge colour in global mode
--label-colour	hex colour	Fallback label colour in global mode
--depth-spacing	number	Adjusts the gap between tree levels
--sibling-spacing	number	Adjusts the gap between siblings
--curve-points	number	Controls curved path smoothness
--straight-points	number	Controls how many points are used for straight paths
--radial-base-angle-deg	number	Sets the starting angle for radial layouts
--radial-sweep-deg	number	Sets the angular sweep for radial layouts
--scale	number	Enlarges SVG geometry, strokes, nodes, and text without changing the tree structure

Colour Palettes

All built-in palettes below are official ColorBrewer, Tableau, or Okabe-Ito palettes. set1 is the default palette.

Custom palettes are also supported:

• In Python, pass a list or tuple of hex colours to LayoutOptions.palette
• On the CLI, pass a comma-separated hex string with --palette, such as #112233,#445566,#778899
• Hex colours are validated before export, so invalid values fail fast

Built-In Palettes

Name	Swatches	Hex codes
set1		#e41a1c #377eb8 #4daf4a #984ea3 #ff7f00 #ffff33 #a65628 #f781bf #999999
set2		#66c2a5 #fc8d62 #8da0cb #e78ac3 #a6d854 #ffd92f #e5c494 #b3b3b3
set3		#8dd3c7 #ffffb3 #bebada #fb8072 #80b1d3 #fdb462 #b3de69 #fccde5 #d9d9d9 #bc80bd #ccebc5 #ffed6f
pastel1		#fbb4ae #b3cde3 #ccebc5 #decbe4 #fed9a6 #ffffcc #e5d8bd #fddaec #f2f2f2
pastel2		#b3e2cd #fdcdac #cbd5e8 #f4cae4 #e6f5c9 #fff2ae #f1e2cc #cccccc
accent		#7fc97f #beaed4 #fdc086 #ffff99 #386cb0 #f0027f #bf5b17 #666666
paired		#a6cee3 #1f78b4 #b2df8a #33a02c #fb9a99 #e31a1c #fdbf6f #ff7f00 #cab2d6 #6a3d9a #ffff99 #b15928
tableau		#1f77b4 #ff7f0e #2ca02c #d62728 #9467bd #8c564b #e377c2 #7f7f7f #bcbd22 #17becf
dark2		#1b9e77 #d95f02 #7570b3 #e7298a #66a61e #e6ab02 #a6761d #666666
scientific		#e69f00 #56b4e9 #009e73 #f0e442 #0072b2 #d55e00 #cc79a7 #000000

Development

For now, use pip install -e .[dev] for local setup and run python -m unittest discover -s tests -v to execute the test suite.

Release Process

This project follows Semantic Versioning:

• MAJOR for breaking API or CLI changes
• MINOR for new backward-compatible features
• PATCH for bug fixes and release-only polish

Before creating a release tag:

1. Update the version in pyproject.toml.
2. Add a short note to CHANGELOG.md.
3. Run the test suite, Ruff, and a build check.
4. Create and push a tag like v0.1.0.
5. Let GitHub Actions publish the tagged build to PyPI.