Points of View: Pathways

Journal name:
Nature Methods
Volume:
13,
Page:
5
Year published:
DOI:
doi:10.1038/nmeth.3699
Published online

Apply visual grouping principles to add clarity to information flow in pathway diagrams.

At a glance

Figures

  1. Rectilinear and curved grids provide overall consistency.
    Figure 1: Rectilinear and curved grids provide overall consistency.

    (a) Fix the number and position of connector points and distribute edges symmetrically in quadrants. (b) Create consistent edge curvature with grids based on circles and rounded rectangles. (c) Nodes positioned on a square grid with circular edge curvature. Connecting adjacent edges with overlapping arrowheads can be locally adjusted from their circular path (dotted line) by vertical stretching (orange) or shrinking (blue) of the edges. (d) Neighbors (gray) of a source node (dark gray) can be aligned horizontally (left) or radially (right). Arrow length can be altered in radial alignment to create groups. Curved (blue) and diagonal (orange) edges are locally adjusted from a 45° guide to avoid overlap between arrowheads.

  2. Creating a clear pathway diagram using a grid and directional information flow.
    Figure 2: Creating a clear pathway diagram using a grid and directional information flow.

    (a) Example of a pathway diagram with unorganized information flow, unnecessary visual detail (e.g., membrane lipids) and no visual continuity along pathways. The dashed line represents the cell nucleus. (b) Pathway from a with redundant visual encodings removed and main points emphasized by visual grouping. Color and shape variations have been removed except for those highlighting a molecule of interest (orange), the products of the pathway (blue) and a membrane protein complex (green). Gray lines are layout guides and would not be included in the final figure; the solid lines provide a grid, and the dotted lines highlight the strong grouping effect of visual connection (circular paths) and proximity.

References

  1. Gehlenborg, N. & Wong, B. Nat. Methods 9, 115 (2012).
  2. Wong, B. Nat. Methods 7, 941 (2010).
  3. Wong, B. Nat. Methods 8, 701 (2011).
  4. Wong, B. Nat. Methods 8, 101 (2011).

Download references

Author information

Affiliations

  1. Barbara J. Hunnicutt is a research assistant at Oregon Health and Science University.

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

Competing financial interests

The authors declare no competing financial interests.

Author details

Additional data