Improving Performance of a leaflet

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I am trying to plot a map using Leaflet on Flexdashboard, output : html. I have a 50,000 data points i needed to plot. i tried using addCircleMarker(lng,lat) and it works in Base R but when the output is generated in an HTML file the performance of the map is so slow. I also tried using leafletOptions(preferCanvas = TRUE)but the performance is still very slow.

I also tried using a different library(leaflet.glify) to improve performance as leaflet.glifycan handle large dataset and used addGlifyPoints(data, color = cbind(0, 0, 0.1), group = "All cases") to plot the map. but i could not run it in an HTML output. It provided me with below error.

pandoc: Could not determine mime type for `/Library/Frameworks/R.framework/Versions/3.5/Resources/library/leaflet.glify/htmlwidgets/Leaflet.glify/src/shader/fragment/dot.glsl'

CallStack (from HasCallStack):

  error, called at src/Text/Pandoc/SelfContained.hs:156:35 in pandoc-1.19.2.1-JIeRA5EnQv74mk86CvVbbp:Text.Pandoc.SelfContained

Error: pandoc document conversion failed with error 1

Execution halted

Any help please.

asked Jan 3 at 3:37

Prabesh Kc

124

what version of pandoc do you have installed? I've found v2.1 solved this type of error.

– SymbolixAU
Jan 3 at 3:40

im using 2.1 but nothing changed for me. Still have issue with performance when plotting 50,000 data points. get_pandoc_version()`` [1] 2.1

– Prabesh Kc
Jan 3 at 9:22

Below is the library and its version [1] googleway_2.7.1 bindrcpp_0.2.2 sf_0.7-2 readxl_1.1.0 [5] colourvalues_0.2.1 leaflet.glify_0.1.1 forcats_0.3.0 stringr_1.3.1 [9] purrr_0.2.5 readr_1.1.1 tidyr_0.8.2 tibble_1.4.2 [13] ggplot2_3.1.0 tidyverse_1.2.1 dplyr_0.7.7 htmltools_0.3.6 [17] htmlwidgets_1.3 rgeos_0.4-2 rgdal_1.3-6 sp_1.3-1 [21] leaflet_2.0.2 flexdashboard_0.5.1.1 pandocfilters_0.1-1

– Prabesh Kc
Jan 3 at 9:40

and my Rmarkdown version is rmarkdown_1.10 @SymbolixAU

– Prabesh Kc
Jan 3 at 9:43

add a comment |

pandoc: Could not determine mime type for `/Library/Frameworks/R.framework/Versions/3.5/Resources/library/leaflet.glify/htmlwidgets/Leaflet.glify/src/shader/fragment/dot.glsl'

CallStack (from HasCallStack):

  error, called at src/Text/Pandoc/SelfContained.hs:156:35 in pandoc-1.19.2.1-JIeRA5EnQv74mk86CvVbbp:Text.Pandoc.SelfContained

Error: pandoc document conversion failed with error 1

Execution halted

Any help please.

asked Jan 3 at 3:37

Prabesh Kc

124

what version of pandoc do you have installed? I've found v2.1 solved this type of error.

– SymbolixAU
Jan 3 at 3:40

im using 2.1 but nothing changed for me. Still have issue with performance when plotting 50,000 data points. get_pandoc_version()`` [1] 2.1

– Prabesh Kc
Jan 3 at 9:22

Below is the library and its version [1] googleway_2.7.1 bindrcpp_0.2.2 sf_0.7-2 readxl_1.1.0 [5] colourvalues_0.2.1 leaflet.glify_0.1.1 forcats_0.3.0 stringr_1.3.1 [9] purrr_0.2.5 readr_1.1.1 tidyr_0.8.2 tibble_1.4.2 [13] ggplot2_3.1.0 tidyverse_1.2.1 dplyr_0.7.7 htmltools_0.3.6 [17] htmlwidgets_1.3 rgeos_0.4-2 rgdal_1.3-6 sp_1.3-1 [21] leaflet_2.0.2 flexdashboard_0.5.1.1 pandocfilters_0.1-1

– Prabesh Kc
Jan 3 at 9:40

and my Rmarkdown version is rmarkdown_1.10 @SymbolixAU

– Prabesh Kc
Jan 3 at 9:43

add a comment |

pandoc: Could not determine mime type for `/Library/Frameworks/R.framework/Versions/3.5/Resources/library/leaflet.glify/htmlwidgets/Leaflet.glify/src/shader/fragment/dot.glsl'

CallStack (from HasCallStack):

  error, called at src/Text/Pandoc/SelfContained.hs:156:35 in pandoc-1.19.2.1-JIeRA5EnQv74mk86CvVbbp:Text.Pandoc.SelfContained

Error: pandoc document conversion failed with error 1

Execution halted

Any help please.

asked Jan 3 at 3:37

Prabesh Kc

124

pandoc: Could not determine mime type for `/Library/Frameworks/R.framework/Versions/3.5/Resources/library/leaflet.glify/htmlwidgets/Leaflet.glify/src/shader/fragment/dot.glsl'

CallStack (from HasCallStack):

  error, called at src/Text/Pandoc/SelfContained.hs:156:35 in pandoc-1.19.2.1-JIeRA5EnQv74mk86CvVbbp:Text.Pandoc.SelfContained

Error: pandoc document conversion failed with error 1

Execution halted

Any help please.

r leaflet r-markdown flexdashboard leaflet.markercluster

asked Jan 3 at 3:37

Prabesh Kc

124

asked Jan 3 at 3:37

Prabesh Kc

124

asked Jan 3 at 3:37

Prabesh Kc

124

asked Jan 3 at 3:37

Prabesh Kc

124

asked Jan 3 at 3:37

Prabesh Kc

124

what version of pandoc do you have installed? I've found v2.1 solved this type of error.

– SymbolixAU
Jan 3 at 3:40

im using 2.1 but nothing changed for me. Still have issue with performance when plotting 50,000 data points. get_pandoc_version()`` [1] 2.1

– Prabesh Kc
Jan 3 at 9:22

Below is the library and its version [1] googleway_2.7.1 bindrcpp_0.2.2 sf_0.7-2 readxl_1.1.0 [5] colourvalues_0.2.1 leaflet.glify_0.1.1 forcats_0.3.0 stringr_1.3.1 [9] purrr_0.2.5 readr_1.1.1 tidyr_0.8.2 tibble_1.4.2 [13] ggplot2_3.1.0 tidyverse_1.2.1 dplyr_0.7.7 htmltools_0.3.6 [17] htmlwidgets_1.3 rgeos_0.4-2 rgdal_1.3-6 sp_1.3-1 [21] leaflet_2.0.2 flexdashboard_0.5.1.1 pandocfilters_0.1-1

– Prabesh Kc
Jan 3 at 9:40

and my Rmarkdown version is rmarkdown_1.10 @SymbolixAU

– Prabesh Kc
Jan 3 at 9:43

add a comment |

what version of pandoc do you have installed? I've found v2.1 solved this type of error.

– SymbolixAU
Jan 3 at 3:40

im using 2.1 but nothing changed for me. Still have issue with performance when plotting 50,000 data points. get_pandoc_version()`` [1] 2.1

– Prabesh Kc
Jan 3 at 9:22

Below is the library and its version [1] googleway_2.7.1 bindrcpp_0.2.2 sf_0.7-2 readxl_1.1.0 [5] colourvalues_0.2.1 leaflet.glify_0.1.1 forcats_0.3.0 stringr_1.3.1 [9] purrr_0.2.5 readr_1.1.1 tidyr_0.8.2 tibble_1.4.2 [13] ggplot2_3.1.0 tidyverse_1.2.1 dplyr_0.7.7 htmltools_0.3.6 [17] htmlwidgets_1.3 rgeos_0.4-2 rgdal_1.3-6 sp_1.3-1 [21] leaflet_2.0.2 flexdashboard_0.5.1.1 pandocfilters_0.1-1

– Prabesh Kc
Jan 3 at 9:40

and my Rmarkdown version is rmarkdown_1.10 @SymbolixAU

– Prabesh Kc
Jan 3 at 9:43

what version of pandoc do you have installed? I've found v2.1 solved this type of error.

– SymbolixAU
Jan 3 at 3:40

im using 2.1 but nothing changed for me. Still have issue with performance when plotting 50,000 data points. get_pandoc_version()`` [1] 2.1

– Prabesh Kc
Jan 3 at 9:22

Below is the library and its version

[1] googleway_2.7.1       bindrcpp_0.2.2        sf_0.7-2              readxl_1.1.0           [5] colourvalues_0.2.1    leaflet.glify_0.1.1   forcats_0.3.0         stringr_1.3.1          [9] purrr_0.2.5           readr_1.1.1           tidyr_0.8.2           tibble_1.4.2          [13] ggplot2_3.1.0         tidyverse_1.2.1       dplyr_0.7.7           htmltools_0.3.6       [17] htmlwidgets_1.3       rgeos_0.4-2           rgdal_1.3-6           sp_1.3-1              [21] leaflet_2.0.2         flexdashboard_0.5.1.1 pandocfilters_0.1-1

– Prabesh Kc
Jan 3 at 9:40

Below is the library and its version

[1] googleway_2.7.1       bindrcpp_0.2.2        sf_0.7-2              readxl_1.1.0           [5] colourvalues_0.2.1    leaflet.glify_0.1.1   forcats_0.3.0         stringr_1.3.1          [9] purrr_0.2.5           readr_1.1.1           tidyr_0.8.2           tibble_1.4.2          [13] ggplot2_3.1.0         tidyverse_1.2.1       dplyr_0.7.7           htmltools_0.3.6       [17] htmlwidgets_1.3       rgeos_0.4-2           rgdal_1.3-6           sp_1.3-1              [21] leaflet_2.0.2         flexdashboard_0.5.1.1 pandocfilters_0.1-1

– Prabesh Kc
Jan 3 at 9:40

and my Rmarkdown version is rmarkdown_1.10 @SymbolixAU

– Prabesh Kc
Jan 3 at 9:43

add a comment |

1 Answer
1

active

oldest

votes

For leaflet.glify you need to set self_contained: false in your yaml header:

---

title: "testing gl"

output: 

  flexdashboard::flex_dashboard:

    vertical_layout: fill

    self_contained: false

---



### Chart 1



```{r}

library(mapview)

library(leaflet)

library(leaflet.glify)

library(sf)



n = 1e5



df1 = data.frame(id = 1:n,

                 x = rnorm(n, 10, 3),

                 y = rnorm(n, 49, 1.8))



pts = st_as_sf(df1, coords = c("x", "y"), crs = 4326)



options(viewer = NULL) # view in browser



system.time({

  m = leaflet() %>%

    addProviderTiles(provider = providers$CartoDB.DarkMatter) %>%

    addGlifyPoints(data = pts, group = "pts") %>%

    addMouseCoordinates() %>%

    setView(lng = 10.5, lat = 49.5, zoom = 6) %>% 

    addLayersControl(overlayGroups = "pts")

})



m

```



### Chart 2



```{r}

plot(cars)

```

answered Jan 8 at 15:51

TimSalabim

3,22911228

Hi @TimSalabim i tried using self_contained : false and it renders the addGlifyPoints . and works perfectly when I open the HTML output within the R.project working directory, but the images are no longer displayed when I send the file to someone. Not sure what is going on there? does anyone have this issue ?

– Prabesh Kc
Jan 10 at 3:58

If your map is called map.html there should also be a folder called map_files where all necessary code is stored (that's what selfcontained false means). You will need to send both the html and the folder to get the map displayed

– TimSalabim
Jan 10 at 8:37

add a comment |

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1 Answer
1

active

oldest

votes

1 Answer
1

active

oldest

votes

For leaflet.glify you need to set self_contained: false in your yaml header:

---

title: "testing gl"

output: 

  flexdashboard::flex_dashboard:

    vertical_layout: fill

    self_contained: false

---



### Chart 1



```{r}

library(mapview)

library(leaflet)

library(leaflet.glify)

library(sf)



n = 1e5



df1 = data.frame(id = 1:n,

                 x = rnorm(n, 10, 3),

                 y = rnorm(n, 49, 1.8))



pts = st_as_sf(df1, coords = c("x", "y"), crs = 4326)



options(viewer = NULL) # view in browser



system.time({

  m = leaflet() %>%

    addProviderTiles(provider = providers$CartoDB.DarkMatter) %>%

    addGlifyPoints(data = pts, group = "pts") %>%

    addMouseCoordinates() %>%

    setView(lng = 10.5, lat = 49.5, zoom = 6) %>% 

    addLayersControl(overlayGroups = "pts")

})



m

```



### Chart 2



```{r}

plot(cars)

```

answered Jan 8 at 15:51

TimSalabim

3,22911228

Hi @TimSalabim i tried using self_contained : false and it renders the addGlifyPoints . and works perfectly when I open the HTML output within the R.project working directory, but the images are no longer displayed when I send the file to someone. Not sure what is going on there? does anyone have this issue ?

– Prabesh Kc
Jan 10 at 3:58

If your map is called map.html there should also be a folder called map_files where all necessary code is stored (that's what selfcontained false means). You will need to send both the html and the folder to get the map displayed

– TimSalabim
Jan 10 at 8:37

add a comment |

For leaflet.glify you need to set self_contained: false in your yaml header:

---

title: "testing gl"

output: 

  flexdashboard::flex_dashboard:

    vertical_layout: fill

    self_contained: false

---



### Chart 1



```{r}

library(mapview)

library(leaflet)

library(leaflet.glify)

library(sf)



n = 1e5



df1 = data.frame(id = 1:n,

                 x = rnorm(n, 10, 3),

                 y = rnorm(n, 49, 1.8))



pts = st_as_sf(df1, coords = c("x", "y"), crs = 4326)



options(viewer = NULL) # view in browser



system.time({

  m = leaflet() %>%

    addProviderTiles(provider = providers$CartoDB.DarkMatter) %>%

    addGlifyPoints(data = pts, group = "pts") %>%

    addMouseCoordinates() %>%

    setView(lng = 10.5, lat = 49.5, zoom = 6) %>% 

    addLayersControl(overlayGroups = "pts")

})



m

```



### Chart 2



```{r}

plot(cars)

```

answered Jan 8 at 15:51

TimSalabim

3,22911228

Hi @TimSalabim i tried using self_contained : false and it renders the addGlifyPoints . and works perfectly when I open the HTML output within the R.project working directory, but the images are no longer displayed when I send the file to someone. Not sure what is going on there? does anyone have this issue ?

– Prabesh Kc
Jan 10 at 3:58

If your map is called map.html there should also be a folder called map_files where all necessary code is stored (that's what selfcontained false means). You will need to send both the html and the folder to get the map displayed

– TimSalabim
Jan 10 at 8:37

add a comment |

For leaflet.glify you need to set self_contained: false in your yaml header:

---

title: "testing gl"

output: 

  flexdashboard::flex_dashboard:

    vertical_layout: fill

    self_contained: false

---



### Chart 1



```{r}

library(mapview)

library(leaflet)

library(leaflet.glify)

library(sf)



n = 1e5



df1 = data.frame(id = 1:n,

                 x = rnorm(n, 10, 3),

                 y = rnorm(n, 49, 1.8))



pts = st_as_sf(df1, coords = c("x", "y"), crs = 4326)



options(viewer = NULL) # view in browser



system.time({

  m = leaflet() %>%

    addProviderTiles(provider = providers$CartoDB.DarkMatter) %>%

    addGlifyPoints(data = pts, group = "pts") %>%

    addMouseCoordinates() %>%

    setView(lng = 10.5, lat = 49.5, zoom = 6) %>% 

    addLayersControl(overlayGroups = "pts")

})



m

```



### Chart 2



```{r}

plot(cars)

```

answered Jan 8 at 15:51

TimSalabim

3,22911228

For leaflet.glify you need to set self_contained: false in your yaml header:

---

title: "testing gl"

output: 

  flexdashboard::flex_dashboard:

    vertical_layout: fill

    self_contained: false

---



### Chart 1



```{r}

library(mapview)

library(leaflet)

library(leaflet.glify)

library(sf)



n = 1e5



df1 = data.frame(id = 1:n,

                 x = rnorm(n, 10, 3),

                 y = rnorm(n, 49, 1.8))



pts = st_as_sf(df1, coords = c("x", "y"), crs = 4326)



options(viewer = NULL) # view in browser



system.time({

  m = leaflet() %>%

    addProviderTiles(provider = providers$CartoDB.DarkMatter) %>%

    addGlifyPoints(data = pts, group = "pts") %>%

    addMouseCoordinates() %>%

    setView(lng = 10.5, lat = 49.5, zoom = 6) %>% 

    addLayersControl(overlayGroups = "pts")

})



m

```



### Chart 2



```{r}

plot(cars)

```

answered Jan 8 at 15:51

TimSalabim

3,22911228

answered Jan 8 at 15:51

TimSalabim

3,22911228

answered Jan 8 at 15:51

TimSalabim

3,22911228

answered Jan 8 at 15:51

TimSalabim

3,22911228

Hi @TimSalabim i tried using self_contained : false and it renders the addGlifyPoints . and works perfectly when I open the HTML output within the R.project working directory, but the images are no longer displayed when I send the file to someone. Not sure what is going on there? does anyone have this issue ?

– Prabesh Kc
Jan 10 at 3:58

If your map is called map.html there should also be a folder called map_files where all necessary code is stored (that's what selfcontained false means). You will need to send both the html and the folder to get the map displayed

– TimSalabim
Jan 10 at 8:37

add a comment |

Hi @TimSalabim i tried using self_contained : false and it renders the addGlifyPoints . and works perfectly when I open the HTML output within the R.project working directory, but the images are no longer displayed when I send the file to someone. Not sure what is going on there? does anyone have this issue ?

– Prabesh Kc
Jan 10 at 3:58

If your map is called map.html there should also be a folder called map_files where all necessary code is stored (that's what selfcontained false means). You will need to send both the html and the folder to get the map displayed

– TimSalabim
Jan 10 at 8:37

Hi @TimSalabim i tried using self_contained : false and it renders the addGlifyPoints . and works perfectly when I open the HTML output within the R.project working directory, but the images are no longer displayed when I send the file to someone. Not sure what is going on there? does anyone have this issue ?

– Prabesh Kc
Jan 10 at 3:58

If your map is called map.html there should also be a folder called map_files where all necessary code is stored (that's what selfcontained false means). You will need to send both the html and the folder to get the map displayed

– TimSalabim
Jan 10 at 8:37

add a comment |

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