How to conditionally highlight points in ggplot2 facet plots - mapping color to column

You should put color=ifelse(y<0, 'red', 'black') inside the aes(), so color will be set according to y values in each facet independently. If color is set outside the aes() as vector then the same vector (with the same length) is used in both facets and then you get error because length of color vector is larger as number of data points.

Then you should add scale_color_identity() to ensure that color names are interpreted directly.

ggplot(df) + geom_point(aes(x, y, color=ifelse(y<0, 'red', 'black'))) + 
   facet_grid(case ~. ,)+scale_color_identity()