map.Rmd

---
title: "Interactive map"
output:
  distill::distill_article:
    toc: true
    toc_depth: 3

---



```{r setup, include=FALSE}
source("readdata.R", local = knitr::knit_global())

```

<font size = 2>
```{r echo=FALSE, layout="l-page"}
filter_slider("Year", "Select year interval", sd, ~Year)
bscols(

filter_select("Pub1", "Select article(s)", sd, ~Pub1),

filter_select("Host", "Host", sd, ~Host),
filter_select("FGSC", "Species", sd, ~FGSC),
filter_select("TRI_genotype", "Select genotype(s)", sd, ~TRI_genotype)
)
```
</font>

```{r echo=FALSE, layout="l-page", fig.height=5}
library(RColorBrewer)
library(htmltools)
pal <- colorFactor("RdYlBu", domain = c("15-ADON", "3-ADON", "DON", "NIV", "DON/NIV",  "NX-2", "NA"))
leaflet(data = sd) %>%
   setView(-0, 15, zoom = 2) %>%
addTiles() %>% 
  addProviderTiles("Esri.WorldImagery", group = "Aerial") %>%
  addProviderTiles("OpenTopoMap", group = "Terrain") %>%
  addScaleBar("bottomright") %>%
  addProviderTiles(providers$CartoDB.Voyager, group = "Default") %>%
  addLayersControl(
    baseGroups = c("Default", "Aerial", "Terrain"),
    overlayGroups = "FGSC",
    options = layersControlOptions(collapsed = TRUE)
  ) %>%

  addCircleMarkers(group = "TRI_genotype", radius = 3, fillOpacity = 0.8,  weight=0.5, color = NA, fillColor = ~pal(TRI_genotype), label = paste(fgsc$FGSC,"- click for details"), popup = paste("Collection code:<b>", fgsc$`Collection code`, "</b>", "<br><i>", fgsc$FGSC,"</i>(", fgsc$TRI_genotype, ")<br>", "Host:", fgsc$Host,"<br>","Location:", fgsc$Country, "<br>","Year of collection:", fgsc$Year, "<br>","Reference:", fgsc$Pub1))%>%
addLegend("bottomleft", pal = pal, values = ~TRI_genotype, title = "TRI genotype",  opacity = 1 )%>%   
  
 addEasyButton(easyButton(
    icon="fa-globe", title="Back to initial view",
    onClick=JS("function(btn, map){ map.setZoom(2); }"))) 


```