Figures related to rankings and heatmap could be transposed.

These are some suggestions regarding visualization defaults.

Working with the ranknings plot i realized that it would be much easier to read if the figure where transposed/rotated so that gene names could be read per line rather than per columns. This would also scale better if one wishes to plot more than 10-30 genes.
There is no inherent information on the y axis that could not be layed out on the x axis.

I also ran in to this format when using the heatmap plotting. Gene names are on the columns rather than rows resulting in a thin matrix and hard to read gene names. As the figure is constructed by using several axis one could transpose the figure having the gene names to the right colorbar on the right and groupings below or ontop of the heatmap. As one is most interested in a dendrogram on the cells (I think?) it could get a nice space on top.

Start by locating the ranking-plot and heatmap plotting entry points, then review how their figures and multiple axes are arranged. Compare the current layout with the requested orientation, including gene-name readability, colorbars, groupings, and dendrogram placement. Done means the visualization defaults are transposed consistently and remain readable for larger gene sets.