library(leaflet)                                                                    
rand_lng <- function(n = 10) rnorm(n, -93.65, .01)                                  
rand_lat <- function(n = 10) rnorm(n, 42.0285, .01)                                 
                                                                                    
random_data <- data.frame(                                                          
  lng = rand_lng(50),                                                                 
  lat = rand_lat(50),                                                                 
  radius = runif(50, 50, 150),                                                        
  circleId = paste0("circle #", 1:50),                                                
  lineId = paste0("circle #", 1:50)                                                   
)                                                                                   
                                                                                    
# display circles (zIndex: 420) above the lines (zIndex: 410), even when added first
leaflet() %>%                                                                       
  addTiles() %>%                                                                      
  # move the center to Snedecor Hall                                                  
  setView(-93.65, 42.0285, zoom = 14) %>%                                             
  addMapPane("ames_lines", zIndex = 410) %>% # shown below ames_circles               
  addMapPane("ames_circles", zIndex = 420) %>% # shown above ames_lines               
  # points above polygons                                                             
  addCircles(                                                                         
    data = random_data, ~lng, ~lat, radius = ~radius, popup = ~circleId,                
    options = pathOptions(pane = "ames_circles")                                        
  ) %>%                                                                               
  # lines in 'ames_lines' pane                                                        
  addPolylines(                                                                       
    data = random_data, ~lng, ~lat, color = "#F00", weight = 20,                        
    options = pathOptions(pane = "ames_lines")                                          
  )                                                                                   

# same example but circles (zIndex: 420) are below the lines (zIndex: 430)          
leaflet() %>%                                                                       
  addTiles() %>%                                                                      
  # move the center to Snedecor Hall                                                  
  setView(-93.65, 42.0285, zoom = 14) %>%                                             
  addMapPane("ames_lines", zIndex = 430) %>% # shown below ames_circles               
  addMapPane("ames_circles", zIndex = 420) %>% # shown above ames_lines               
  # points above polygons                                                             
  addCircles(                                                                         
    data = random_data, ~lng, ~lat, radius = ~radius, popup = ~circleId,                
    options = pathOptions(pane = "ames_circles")                                        
  ) %>%                                                                               
  # lines in 'ames_lines' pane                                                        
  addPolylines(                                                                       
    data = random_data, ~lng, ~lat, color = "#F00", weight = 20,                        
    options = pathOptions(pane = "ames_lines")                                          
  )