School of Data Science, University of Virginia, Charlottesville, Virginia, United States of America.
Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America.
PLoS One. 2024 May 31;19(5):e0304632. doi: 10.1371/journal.pone.0304632. eCollection 2024.
We propose a fold change transform that demonstrates a combination of visualization properties exhibited by log and linear plots of fold change. A fold change visualization should ideally exhibit: (1) readability, where fold change values are recoverable from datapoint position; (2) proportionality, where fold change values of the same direction are proportionally distant from the point of no change; (3) symmetry, where positive and negative fold changes of the same magnitude are equidistant to the point of no change; and (4) high dynamic range, where datapoint values are distinguishable across orders of magnitude within a fixed plot area and pixel resolution. A linear visualization has readability and partial proportionality but lacks high dynamic range and symmetry (because negative direction fold changes are bound between [0, 1] while positive are between (1, ∞)). Log plots of fold change have partial readability, high dynamic range, and symmetry, but lack proportionality because of the log transform. We outline a new transform, named mirrored axis distortion of fold change (MAD-FC), that extends a linear visualization of fold change data to exhibit readability, proportionality, and symmetry (but still has the limited dynamic range of linear plots). We illustrate the use of MAD-FC with biomedical data using various fold change plots. We argue that MAD plots may be a more useful visualization than log or linear plots for applications that do not require a high dynamic range (less than 8 units in log2 space).
我们提出了一种折叠变化变换，它展示了对数和线性折叠变化图所表现出的可视化属性的组合。折叠变化的可视化理想情况下应该表现出：（1）可读取性，其中折叠变化值可以从数据点位置恢复；（2）比例性，相同方向的折叠变化值与无变化点成比例距离；（3）对称性，相同大小的正折叠变化和负折叠变化与无变化点等距；（4）高动态范围，其中在固定的绘图区域和像素分辨率内，数据点值在数量级上可区分。线性可视化具有可读取性和部分比例性，但缺乏高动态范围和对称性（因为负向折叠变化值在 [0,1] 之间，而正向折叠变化值在 (1,∞) 之间）。折叠变化的对数图具有部分可读取性、高动态范围和对称性，但由于对数变换而缺乏比例性。我们概述了一种新的变换，称为折叠变化的镜像轴扭曲（MAD-FC），它扩展了折叠变化数据的线性可视化，以表现出可读取性、比例性和对称性（但仍然具有线性图的有限动态范围）。我们使用各种折叠变化图展示了 MAD-FC 在生物医学数据中的应用。我们认为，对于不需要高动态范围（对数 2 空间中小于 8 个单位）的应用程序，MAD 图可能比对数或线性图更有用。
