The visualization of complex and multi-dimensional data sets in a meaningful way is a difficult process. Often, bar graphs or scatter plots do not sufficiently demonstrate the complexity or nuance of the data, particularly in a functional connected network (i.e. gene networks, behavioral endpoints, circulating hormones). Here, we provide a method to plot various data types across multiple measures on the same figure.
While the scripts used to create these figures are our own, the software used to create them is MATLAB. You are free to use or edit these scripts but we require acknowledgment when published or presented.
PDF Samuel V Scarpino, Ross Gillette, and David Crews. 2014. multiDimBio: An R Package for the Design, Analysis, and Visualization of Systems Biology Experiments. arXiv:1404.0594v1 [q-bio.QM].
PDF David Crews, Ross Gillette, Samuel V. Scarpino, Mohan Manikkam, Marina I. Savenkova, and Michael K. Skinner. 2012. Epigenetic transgenerational inheritance of altered stress responses. PNAS. 109 (23): 9143–9148.
Creation of functional landscapes is simple. There are 6 necessary files that need to be within the same directory (folder) for the script to work.
Download the necessary files here.
Only 1 of these files needs to be edited. The “X_Template.m” files are what you will interact with, where X is the number of peaks or troughs that will be plotted by the script. These template files are listed below with example plots.
Enter your data
Within each template file is the following code:
% define coordinates and heights of nuclei
% Change za, zb, zc… zn for the height of each node
xa = 20; ya = 20; za = 100;
xb = 20; yb = -20; zb = -100;
xc = -20; yc = -20; zc = 100;
xe = -20; ye = 20; ze = -100;
The text shown in black is what dictates the height of the peak. You can use raw averages, percent of a control group, or any other scaling method that you desire.
You may want to change the scale of the Y-axis for the plot (i.e. your scale is from 10 to 30, not -100 to 100 as shown in the templates). The code that needs to be changed is below, shown in black located near the end of the script.
Number of Peaks