How do I increase the minimum dot size in Seurat's DotPlot function?

Question

I want to use the DotPlot function from Seurat v3 to visualise the expression of some genes across clusters. However when the expression of a gene is zero or very low, the dot size is so small that it is not clearly visible when printed on paper. Please is there a possibility to increase the minimum dot size in the DotPlot function to make the dot sizes more visible when printed?

For example, I would like to have a minimum dot size set to be like

from this publication

Rather than:

from this other publication

Thank you in advance for your helpful hint.

Answer 1

Did you try to use DotPlot(..., scale.by = "size")?

In contrast to the default scale.by= "radius", this will link the area (==2*pi*r^2), not the radius, of the circles to the fraction of cells expressing the feature. This corresponds much better to our perception of size and will make differences in low values easier to see.

Reading ?Seurat::DotPlot the scale.min parameter looked promising but looking at the code it seems to censor the data as well.

Since Seurat's plotting functionality is based on ggplot2 you can also adjust the color scale by simply adding scale_fill_viridis() etc. to the returned plot. This might also work for size. Try something like:

DotPlot(...) + scale_size(range = c(5, 10)) # will likely warn about supplying the same scale twice

Apart from this, Seurat's plotting system is not very hackable and I find it much easier to extract the relevant data and plot them myself with ggplot2.

Yet another comment: Your plot with the strong differences looks much more convincing to me wrt. to the marker property of these genes than the cited plot.

Answer 2

You can define your breaks with:

p + scale_size(breaks = c(0, 25, 50, 75))

You can adjust the size of the points with:

p + scale_size(range = c(1,8))     # Note: c(1,6) is the default

For more info, see ??scale_size