Page 5: Figure 3

[LTLA]

Can't read any of the legend text.

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Plots are shown using all genes (a-c) and cell cycle genes only (d-f) using PCA (a,d), t-SNE (b,e) and diffusion maps (c,f).

Need to mention what the points actually represent:

Plots are shown using all genes (a-c) and cell cycle genes only (d-f) using PCA (a,d), t-SNE (b,e) and diffusion maps (c,f), where each point in each plot represents a cell.

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... points are coloured by the expression of CCND2 (ENSG00000118971), a gene associated with the G1/S phase transition of the cell cycle.

Don't need ENSEMBL ID, no one cares:

... points are coloured by the expression of CCND2 (a gene associated with the G1/S phase transition of the cell cycle) in each cell.

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With the plotExpression function, expression for sets of genes can be plotted against any cell metadata variables or the expression of a given gene (g).

Need to mention what the plot actually shows:

With the plotExpression function, gene expression can be plotted against any cell metadata variables or the expression of another gene - here, expression for the CD86, IGH44 and IGHV4-34 genes in each cell is plotted against the patient of origin (g).

[davismcc]

All fixed up now, and much better, I think.