Subset Cells in ScatterPie

[ABauer26]

Hi Marc,

I appreciate working with the package SPOTlight and have a question about plotting specific cell types in the spatial scatter pie function and maintaining the original cell frequencies per spot.
Regarding this function:
plotSpatialScatterpie(
x,
y,
cell_types = colnames(y),
img = FALSE,
slice = NULL,
scatterpie_alpha = 1,
pie_scale = 0.4,
degrees = NULL,
axis = NULL,
...
)

In this function, under cell_types, I would like to only include in my spatial scatter pie cell types such as - cell_types = c("B Cells", "TFH", "CD8 T Cells"), however this coerces these three cell types to occupy a total of 100% of each spatial spot.

Is there an easier way to plot only 3 cell types from 13 cell types total, but ignore the other cell types present (without manually setting the color palette as gray for all cell types not of interest)?

Thanks!

[MarcElosua]

Hi @ABauer26

That is a great question, unfortunately that is not a feature of plotSpatialScatterpie. However, a quick workaround could be to create an extra column in your metadata called other which adds up the proportions of the cell types you are not interested in and then pass cell_types = c("B Cells", "TFH", "CD8 T Cells", "other").

Hope this helps!