General plots / Expression dot plot
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Each dot is a group × gene combination: its size is the share of cells in the group expressing the gene (above the threshold) and its colour the mean expression.
By default colours are z-scores of each gene across groups, so they compare one gene between groups; colours of different genes are not directly comparable.
Mean expression can be taken over all cells (reflecting both share and level, the common choice) or over expressing cells only (level alone).
Use normalised expression (for example log1p(CP10k)); raw counts make cells with different sequencing depth incomparable. Very low shares can be hidden with the threshold for dots.
Fraction expressing = cells with expression above the threshold / cells in the group; mean expression is the arithmetic mean (as in common single-cell dot plots); z-scores use the sample standard deviation (n − 1).
Up to 150 genes and 200 groups.
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