The bitmap goes below the base layer, and the markers remain higher: xIndex is ignored

Question

I am creating a simple Shiny + Leaflet R application to navigate the map on which the raster (from the raster package) is built with the useful addRasterImage() function. The code is largely based on Leaflet's own examples. However, I am facing some layering issues: the bitmap is somehow displayed below the fragments every time I reload the fragments, even if I set a negative zIndex . This does not happen for markers. See the attached code. An example input file is here , 366 KB.

 #### ###### YOU CAN SKIP THIS, THE PROBLEM LIES BELOW ###### #### library(shiny) library(leaflet) library(RColorBrewer) library(raster) selrange <- function(r, min, max) { #Very fast way of selecting raster range, even faster than clamp. #http://stackoverflow.com/questions/34064738/fastest-way-to-select-a-valid-range-for-raster-data rr <- r[] rr[rr < min | rr > max] <- NA r[] <- rr r } llflood <- raster("example_flooding_posmall.nc") ext <- extent(llflood) flood <- projectRasterForLeaflet(llflood) floodmin <- cellStats(flood, min) floodmax <- cellStats(flood, max) tiles <- c("Hydda.Base", "Hydda.Full", "Esri.WorldImagery", "Esri.WorldTopoMap" ) ui <- bootstrapPage( tags$style(type = "text/css", "html, body {width:100%;height:100%}"), leafletOutput("map", width = "100%", height = "100%"), absolutePanel(top = 10, right = 10, sliderInput("range", "Return Period (years)", floor(floodmin), ceiling(floodmax), value = c(floor(floodmin), ceiling(floodmax)), step = 1 ), selectInput("colors", "Color Scheme", rownames(subset(brewer.pal.info, category %in% c("seq", "div"))) ), selectInput("tiles", "Background", tiles ), checkboxInput("legend", "Show legend", TRUE)) ) server <- function(input, output, session) { # Reactive expression for the data subsetted to what the user selected filteredData <- reactive({ selrange(flood, input$range[1], input$range[2]) }) # This reactive expression represents the palette function, # which changes as the user makes selections in UI. colorpal <- reactive({ colorNumeric(input$colors, values(filteredData()), na.color = NA) }) ###### ###### THE INTERESTING PART IS HERE ###### ###### output$map <- renderLeaflet({ # Use leaflet() here, and only include aspects of the map that # won't need to change dynamically (at least, not unless the # entire map is being torn down and recreated). leaflet() %>% fitBounds(ext[1], ext[3], ext[2], ext[4]) }) observe({ #Observer to edit tiles selectedTiles <- input$tiles leafletProxy("map") %>% clearTiles() %>% addProviderTiles(selectedTiles, providerTileOptions(zIndex=-10, continuousWorld=FALSE), group="base") }) observe({ #Observer to edit colors and valid range filtdata <- filteredData() pal <- colorpal() leafletProxy("map") %>% clearImages() %>% addRasterImage(filtdata, opacity=0.7, project=FALSE, colors=pal, group="overlay") %>% addMarkers(lng=8.380508, lat=45.18058, popup="This marker stays above, the raster sinks below every time I load a new tile set") }) ###### ###### THE INTERESTING PART ENDS HERE ###### ###### observe({ #Observer to show or hide the legend inputlegend <- input$legend proxy <- leafletProxy("map") # Remove any existing legend, and only if the legend is # enabled, create a new one. proxy %>% clearControls() if (inputlegend) { pal <- colorpal() proxy %>% addLegend(position = "bottomright", pal = pal, values = values(filteredData()), opacity=1 ) } }) cat("Clicked point:\tLon\t\tLat\t\tValue\n") observe({ #Observe to show clicked points x = as.double(unlist(input$map_click)[2]) if(!is.null(x)) { y = unlist(input$map_click)[1] val = extract(llflood, cellFromXY(llflood, c(x, y))) if (!is.na(val)) cat("\t\t", x, "\t", y, "\t", val, "\n") } }) } ## RUN: shinyApp(ui, server) 

Answer 1

I also have this problem, but your question is the only link to it that I can find.

The only workaround I could find was also to redraw the tiles in the raster observer, for example.

 observe({ #Observer to edit colors and valid range selectedTiles <- input$tiles filtdata <- filteredData() pal <- colorpal() leafletProxy("map") %>% clearTiles() %>% addProviderTiles(selectedTiles, providerTileOptions(zIndex=-10, continuousWorld=FALSE), group="base") clearImages() %>% addRasterImage(filtdata, opacity=0.7, project=FALSE, colors=pal, group="overlay") %>% addMarkers(lng=8.380508, lat=45.18058, popup="This marker stays above, the raster sinks below every time I load a new tile set") })