Perhaps start with a simple example.
Create a three-column spreadsheet or tab-delimited text file (matrix) that contains three column headers for each of the three principle components: PC1, PC2, PC3. These are the three axes of the cube. Underneath the headers, you have a three-dimensional data point that shows the principle component score of that gene/sample.
Once you import this, you have a scatterplot that you can begin to think about labeling, by adding a fourth and subsequent columns to your matrix file.
In the fourth column, you can add labels for each point, such as gene name. Reimport the file and move the mouse pointer over each datapoint.
In the fifth column, you can add a category label to each point. You might have three category labels, one for each of the three samples. Each point is assigned a specific sample label.
As you mouse over the datapoints, you'll see the gene name and sample label. Additionally, category labels are used to color points. In this way, you can see clusters of datapoints, especially after you manipulate the cube's rotation in the browser window.
You can add sixth and subsequent columns to your matrix, to include additional categorizations. For example, you might have treatment categories, dosage range categories, timepoint categories, etc. Each have their own color scheme. You can switch between these categorizations with the pull-down menu at the bottom of the screen, and quickly see any clustering by color and spacial position.
Hi Alex, I find Cubemaker super interesting. Is something you developed? I've being fighting with rgl and webGL for weeks in R, and by chance I found your answer. I tried to find more information about Cubemaker in the web, but I couldn't find any details. I was wondering where the imported data is hosted, how long are the exported links available, and what about privacy policies. I'd like to use Cubemaker to create and host some plots we want to publish as supplementary material in a paper, so copyright and stability of the links are of major importance to me. I would be very grateful for any complementary information you could give me. Thanks a lot!
Source is available here: https://github.com/alexpreynolds/cubemaker
The front-end is everything in this repository but the
cubemaker-viz-proxyfolder.To host Cubemaker data locally, you'll need a host with node.js, R (with
rgl), and a working X11 display buffer running the proxy service in thecubemaker-viz-proxyfolder. See the README in that folder.I don't have any documentation on setting this up locally, but if you have some command-line chops, you could probably figure this out pretty easily. To keep your data secure, you can keep the server within a private network, but I don't know how that would work for a paper.
If you use my code to visualize your data, I'd appreciate a cite, of course. Feel free to contact me off-list if that's doable.