Points of view: Multidimensional data

Journal name:
Nature Methods
Volume:
10,
Page:
595
Year published:
DOI:
doi:10.1038/nmeth.2531
Published online

Visually organize complex data by mapping them onto familiar representations of biological systems.

At a glance

Figures

  1. Dimensions can be encoded as spatial or visual elements, such as along x and y axes or by color, size or symbol.
    Figure 1: Dimensions can be encoded as spatial or visual elements, such as along x and y axes or by color, size or symbol.

    The number of dimensions and the selection and layering of encodings can have a profound effect on clarity.

  2. Overview of the impact of a drug class on a signaling network in different cell types.
    Figure 2: Overview of the impact of a drug class on a signaling network in different cell types.

    Colored circles encode EC50 and percent inhibition using the scheme in Figure 3c. Adapted from ref. 1.

  3. Design schematic for Figure 2, showing data structure, variable type and visual mapping.
    Figure 3: Design schematic for Figure 2, showing data structure, variable type and visual mapping.

    (a) Identification of nested data dimensions informs the levels of organization in the figure. (b) Data types and encodings used. (c) The protein dimension is spatially encoded into a diagram of the signaling network and tabulated by experimental condition. The adjacency of proteins signifies involvement in the same pathway, and vertical position relates to intracellular position. Protein nodes are combined into shapes. Perceptually accurate size and hue encodings2 are used for EC50 and percent inhibition.

References

  1. Bodenmiller, B. et al. Nat. Biotechnol. 30, 858867 (2012).
  2. Gehlenborg, N. & Wong, B. Nat. Methods 9, 769 (2012).

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Author information

Affiliations

  1. Martin Krzywinski is a staff scientist at Canada's Michael Smith Genome Sciences Centre.

  2. Erica Savig is a PhD candidate in Cancer Biology in the laboratory of Garry P. Nolan at Stanford University.

Competing financial interests

The authors declare no competing financial interests.

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