VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays

Kestler, Hans A.; Müller, André Frotta; Kraus, Johann M.; Buchholz, Malte; Gress, Thomas M.; Liu, Hongfang; Kane, David W.; Zeebèrg, Barry R.; Weinstein, John N.

doi:10.1186/1471-2105-9-67

Cited by 98 publications

(93 citation statements)

References 15 publications

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“…Moreover, we also envision extensions to the language of spider diagrams, proof search automation, use of Speedith in practical settings [16,6], and a study of scalability of proofs and their visualisation in Speedith.…”

Section: Resultsmentioning

confidence: 99%

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Speedith: A Reasoner for Spider Diagrams

Urbas

Jamnik

2015

J of Log Lang and Inf

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In this paper, we introduce Speedith which is an interactive diagrammatic theorem prover for the well-known language of spider diagrams. Speedith provides a way to input spider diagrams, transform them via the diagrammatic inference rules, and prove diagrammatic theorems. Speedith's inference rules are sound and complete, extending previous research by including all the classical logic connectives. In addition to being a stand-alone proof system, Speedith is also designed as a program that plugs into existing general purpose theorem provers. This allows for other systems to access diagrammatic reasoning via Speedith, as well as a formal verification of diagrammatic proof steps within standard sentential proof assistants. We describe the general structure of Speedith, the diagrammatic language, the automatic mechanism that draws the diagrams when inference rules are applied on them, and how formal diagrammatic proofs are constructed.

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Section: Resultsmentioning

confidence: 99%

“…Speedith then makes this the initial goal of the current proof, which is immediately visualised 16 in the proof panel. Fig.…”

mentioning

confidence: 99%

Speedith: A Reasoner for Spider Diagrams

Urbas

Jamnik

2015

J of Log Lang and Inf

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“…In criminal investigations, sets represent organizations to which people (the data items) belong or locations they frequent [12]. Similar complex data occur in biological settings where data items are genes, whilst sets represent shared features of the genes [16]. We also find Euler diagrams being used in both art and architecture [2], education [14], computer file organisation [11] and classification systems [35].…”

Section: Introductionmentioning

confidence: 99%

“…Reflecting the importance of understanding such data there have been a large number of techniques proposed for visualizing it such as [1,10,16,25,28,29,32,33,39]. Most of these techniques represent the sets using Euler diagrams.…”

Section: Introductionmentioning

confidence: 99%

The impact of topological and graphical choices on the perception of Euler diagrams

Blake

Rodgers

Howse

2016

Information Sciences

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This paper establishes the impact of topological and graphical properties on the comprehension of Euler diagrams. To-date, various studies have examined the impact of individual properties of Euler diagrams, such as curve shape and orientation. This has allowed us to establish guides for using these properties such as 'draw Euler diagrams with circles' and 'draw Euler diagrams without regard to orientation'. However, until the work described here, questions still remain, for example 'do these guides, when combined, make a significant difference to real-world Euler diagrams?', and if so, 'should they be used by those visualizing set data with Euler diagrams?' To answer these questions an empirical study was conducted to compare Euler diagrams that have been drawn by others for their real-world data, against versions that adhere to all of the guides in combination. The study establishes that both the accuracy and the speed with which information is derived from Euler diagrams is significantly improved when Euler diagrams adhere, where possible, to all the guides. The improvement is considerable when using the guided diagrams, with on average, the error rate being more than halved from 21.4% to 10.3%, and a 9 second improvement in the average time taken, from 34.2 seconds to 24.9 seconds. As Euler diagrams are regularly used to visualize information in a multitude of areas, ranging from crime control to social network analysis, our results indicate that applying the guides to these diagrams will improve the ability of users to accurately and quickly extract information.

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“…Area-proportional Venn diagrams, where the areas of the regions formed from curves are equal to an area specification, are widely used when visualizing numerical data [6,8,7]. An example of such a diagram is shown in Figure 1, adapted from [10].…”

Section: Introductionmentioning

confidence: 99%

Drawing Area-Proportional Venn-3 Diagrams with Convex Polygons

Rodgers

Flower

Howse

2010

Diagrammatic Representation and Inference

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Abstract. Area-proportional Venn diagrams are a popular way of visualizing the relationships between data sets, where the set intersections have a specified numerical value. In these diagrams, the areas of the regions are in proportion to the given values. Venn-3, the Venn diagram consisting of three intersecting curves, has been used in many applications, including marketing, ecology and medicine. Whilst circles are widely used to draw such diagrams, most area specifications cannot be drawn in this way and, so, should only be used where an approximate solution is acceptable. However, placing different restrictions on the shape of curves may result in usable diagrams that have an exact solution, that is, where the areas of the regions are exactly in proportion to the represented data. In this paper, we explore the use of convex shapes for drawing exact area proportional Venn-3 diagrams. Convex curves reduce the visual complexity of the diagram and, as most desirable shapes (such as circles, ovals and rectangles) are convex, the work described here may lead to further drawing methods with these shapes. We describe methods for constructing convex diagrams with polygons that have four or five sides and derive results concerning which area specifications can be drawn with them. This work improves the state-of-the-art by extending the set of area specifications that can be drawn in a convex manner. We also show how, when a specification cannot be drawn in a convex manner, a non-convex drawing can be generated.

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VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays

Cited by 98 publications

References 15 publications

Speedith: A Reasoner for Spider Diagrams

Speedith: A Reasoner for Spider Diagrams

The impact of topological and graphical choices on the perception of Euler diagrams

Drawing Area-Proportional Venn-3 Diagrams with Convex Polygons

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