Identify position of a click on a raster in leaflet, in R
<p>I am plotting a large lat-lon NetCDF <code>raster</code> over an R <code>leaflet</code> map using <code>shinydashboard</code>. When I click on the map, a popup comes out and shows row, column, lat-lon position and value of the clicked raster point. (See reproducible code below)</p>

<p>The problem is that I am experiencing a shift in the raster if the raster is large enough. For example, here I clicked on a point which should have a value, but the result is that the identified point is the one above.</p>

<p><a href="https://i.stack.imgur.com/eP4kL.png" rel="noreferrer"><img src="https://i.stack.imgur.com/eP4kL.png" alt="enter image description here"></a></p>

<p>I believe this has to do with the fact that the raster used by <code>leaflet</code> is projected, while the raw data I use to identify the points is Lat-Lon, since the clicked point is returned as Lat-Lon by <code>leaflet</code>. I cannot use the projected file (<code>depth</code>) since its units are in meters, not degrees!
Even if I tried to reproject those meters to degrees, I got a shift.</p>

<p>Here is a basic runnable example of the code:</p>

<pre><code>#Libraries
library(leaflet)
library(raster)
library(shinydashboard)
library(shiny)

#Input data
download.file("https://www.dropbox.com/s/y9ekjod2pt09rvv/test.nc?dl=0", destfile="test.nc")
inputFile    = "test.nc"
inputVarName = "Depth"
lldepth &lt;- raster(inputFile, varname=inputVarName)
lldepth[Which(lldepth&lt;=0, cells=T)] &lt;- NA #Set all cells &lt;=0 to NA
ext &lt;- extent(lldepth)
resol &lt;- res(lldepth)
projection(lldepth) &lt;- "+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"

#Project for leaflet
depth &lt;- projectRasterForLeaflet(lldepth)

#Prepare UI
sbwidth=200
sidebar &lt;- dashboardSidebar(width=sbwidth)
body &lt;- dashboardBody(
          box( #https://stackoverflow.com/questions/31278938/how-can-i-make-my-shiny-leafletoutput-have-height-100-while-inside-a-navbarpa
            div(class="outer",width = NULL, solidHeader = TRUE, tags$style(type = "text/css", paste0(".outer {position: fixed; top: 50px; left: ", sbwidth, "px; right: 0; bottom: 0px; overflow: hidden; padding: 0}")),
            leafletOutput("map", width = "100%", height = "100%")
            )
          )
        )
ui &lt;- dashboardPage(
  dashboardHeader(title = "A title"),
  sidebar,
  body
)
#
#Server instance
server &lt;- function(input, output, session) {
  output$map &lt;- renderLeaflet({#Set extent
    leaflet()  %&gt;%
      fitBounds(ext[1], ext[3], ext[2], ext[4])
  })

  observe({#Observer to show Popups on click
    click &lt;- input$map_click
    if (!is.null(click)) {
      showpos(x=click$lng, y=click$lat)
    }
  })

  showpos &lt;- function(x=NULL, y=NULL) {#Show popup on clicks
    #Translate Lat-Lon to cell number using the unprojected raster
    #This is because the projected raster is not in degrees, we cannot use it!
    cell &lt;- cellFromXY(lldepth, c(x, y))
    if (!is.na(cell)) {#If the click is inside the raster...
      xy &lt;- xyFromCell(lldepth, cell) #Get the center of the cell
      x &lt;- xy[1]
      y &lt;- xy[2]
      #Get row and column, to print later
      rc &lt;- rowColFromCell(lldepth, cell)
      #Get value of the given cell
      val = depth[cell]
      content &lt;- paste0("X=",rc[2],
                        "; Y=",rc[1],
                        "; Lon=", round(x, 5),
                        "; Lat=", round(y, 5),
                        "; Depth=", round(val, 1), " m")
      proxy &lt;- leafletProxy("map")
      #add Popup
      proxy %&gt;% clearPopups() %&gt;% addPopups(x, y, popup = content)
      #add rectangles for testing
      proxy %&gt;% clearShapes() %&gt;% addRectangles(x-resol[1]/2, y-resol[2]/2, x+resol[1]/2, y+resol[2]/2)
    }
  }

  #Plot the raster
  leafletProxy("map") %&gt;%
    addRasterImage(depth, opacity=0.8, project=FALSE, group="Example", layerId="Example", colors=colorNumeric(terrain.colors(10), values(depth), na.color = "black"))
}


print(shinyApp(ui, server))
</code></pre>

<p>How can I correctly identify the points, if the raster is large?</p>

<p>EDIT:
I also wanted to provide some additional links to (possibly) related documentation or questions:</p>

<ul>
<li><a href="https://stackoverflow.com/questions/33742107/raster-image-seems-to-be-shifted-using-leaflet-for-r?rq=1">Raster image seems to be shifted using leaflet for R</a></li>
<li><a href="https://stackoverflow.com/questions/34583442/r-for-leaflet-redirect-when-clicking-on-raster-image">R for leaflet redirect when clicking on raster image</a></li>
<li><a href="https://gis.stackexchange.com/questions/183918/is-it-possible-to-use-a-rasterclick-event-within-an-interactive-leaflet-map">https://gis.stackexchange.com/questions/183918/is-it-possible-to-use-a-rasterclick-event-within-an-interactive-leaflet-map</a></li>
<li><a href="https://stackoverflow.com/questions/28938642/marker-mouse-click-event-in-r-leaflet-for-shiny">marker mouse click event in R leaflet for shiny</a></li>
</ul>