Hey,
Use colorFactor function.
Check this example.
pal <- colorFactor(c("navy", "red"), domain = c("ship", "pirate"))
leaflet(df) %>% addTiles() %>%
  addCircleMarkers(
    radius = ~ifelse(type == "ship", 6, 10),
    color = ~pal(type),
    stroke = FALSE, fillOpacity = 0.5
  )