Drawing non-layered tidy trees in linear time

Ploeg, Auke van der

doi:10.1002/spe.2213

Cited by 9 publications

(4 citation statements)

References 26 publications

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“…We use utility functions from the D3 library [5] and the D3 Flextree plugin, which extends the tree layout module of D3 to produce a compact layout with variable width nodes [71]. Finally, the Trrack library is used to record and display interaction provenance [17].…”

Section: Methodsmentioning

confidence: 99%

Aardvark: Composite Visualizations of Trees, Time-Series, and Images

Lange,

Judson-Torres,

Zangle

et al. 2024

Preprint

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How do cancer cells grow, divide, proliferate and die? How do drugs influence these processes? These are difficult questions that we can attempt to answer with a combination of time-series microscopy experiments, classification algorithms, and data visualization. However, collecting this type of data and applying algorithms to segment and track cells and construct lineages of proliferation is error-prone; and identifying the errors can be challenging since it often requires cross-checking multiple data types. Similarly, analyzing and communicating the results necessitates synthesizing different data types into a single narrative.State-of-the-art visualization methods for such data use independent line charts, tree diagrams, and images in separate views. However, this spatial separation requires the viewer of these charts to combine the relevant pieces of data in memory.To simplify this challenging task, we describe design principles for weaving cell images, time-series data, and tree data into a cohesive visualization. Our design principles are based on choosing a primary data type that drives the layout and integrates the other data types into that layout. We then introduce Aardvark, a system that uses these principles to implement novel visualization techniques. Based on Aardvark, we demonstrate the utility of each of these approaches for discovery, communication, and data debugging in a series of case studies.

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Section: Methodsmentioning

confidence: 99%

Aardvark: Composite Visualizations of Trees, Time-Series, and Images

Lange,

Judson-Torres,

Zangle

et al. 2024

Preprint

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show abstract

“…We present here briefly the algorithm that allows obtaining the nonlayered tidy tree layout (proposed by van der Ploeg 2014 ), and we give illustrative examples of its use in the next section. We take as a starting point a tree plotted as in figure 1 B (left).…”

Section: New Approachesmentioning

confidence: 99%

“…For details on the algorithm and demonstration of its linearity, refer to the original article ( van der Ploeg 2014 ).…”

Section: New Approachesmentioning

confidence: 99%

“…1 A- 2 ), no layout was made accessible to phylogeneticists to make a better use of these empty areas. Such a layout, however, exists: the nonlayered tidy tree layout, which can be drawn in linear time following the Reingold–Tilford algorithm( Reingold and Tilford 1981 ) and its extension to trees with branch lengths (i.e., nonlayered, van der Ploeg 2014 ).…”

Section: Introductionmentioning

confidence: 99%

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tidy tree: A New Layout for Phylogenetic Trees

Penel

Vienne

2022

Molecular Biology and Evolution

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Many layouts exist for visualising phylogenetic trees, allowing to display the same information (evolutionary relationships) in different ways. For large phylogenies, the choice of the layout is a key element, because the printable area is limited, and because interactive on-screen visualizers can lead to unreadable phylogenetic relationships at high zoom levels. Visual inspection of available layouts for rooted trees reveal large empty areas that one may want to fill in order to use less drawing space, and eventually gain in readability. This can be achieved by the non-layered tidy tree layout algorithm that was proposed earlier but was never used in a phylogenetic context so far. Here, we present its implementation and we demonstrate its advantages on simulated and biological data (the measles virus phylogeny). Our results call for the integration of this new layout in phylogenetic software. We implemented the non-layered tidy tree layout in R language as a standalone function (available at https://github.com/damiendevienne/non-layered-tidy-trees, as an option in the tree plotting function of the R package ape, and in the recent tool for visualising reconciled phylogenetic trees thirdkind (https://github.com/simonpenel/thirdkind/wiki).

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Detailed visualization of communication network topologies

Zipper

Diedrich

2017

IFAC-PapersOnLine

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Drawing non-layered tidy trees in linear time

Cited by 9 publications

References 26 publications

Aardvark: Composite Visualizations of Trees, Time-Series, and Images

Aardvark: Composite Visualizations of Trees, Time-Series, and Images

tidy tree: A New Layout for Phylogenetic Trees

Detailed visualization of communication network topologies

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