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I got data (1503, 38697) (cell(datapoint), genes(features)), each elements has integer values (gene expression).

so something like

           gene 1           gene 2          gene 3
cell 1        10                 0              20
cell 2        20                10              50

I plotted some data points as histogram for each cell (x axis for gene (features), y axis for value ), but it takes too much time with matplotlib.

One of my boss said I should make this plot as 3D, recommend to split x-axis (x-axis for gene (features)). And make sure not to loose x-axis information.

How should I split x-axis?

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1 Answer 1

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What your boss means by 'split x-axis' is not clear for me either. Might be best to ask that person.

Will your datapoints be like $\left(X,\,Y,\,Z\right)=\left(10, \,0,\,20\right)$, $\left(20,\,10,\,50\right)$? In this case the data naturally lies in the positive sector of XYZ plot.

I would perhaps think of doing a radial transform and plotting radius as color and angles as coordinates on paper. Even better choice might be something like https://en.wikipedia.org/wiki/Stereographic_projection, where you still plot radius $r=\sqrt{X^2+Y^2+Z^2}$ as color, and the other two coordinates as positions on the piece of paper. I would probably have the north pole axis to be $\left(1,1,1\right)$ so that there is symmetry between the three axis.

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