An informative message is now printed (rather than a stop action) if …

…the Lifemap server cannot be reached. The vignette is also managed in this case.

R/build_Lifemap.R

@@ -34,35 +34,37 @@
 #' LM <- build_Lifemap(eukaryotes_80, "fr")
 #' }
 build_Lifemap <- function(df, basemap = c("ncbi", "base", "fr", "virus"), verbose = TRUE) {
-
-    basemap <- match.arg(arg = basemap, choices = basemap)
-    if(is.null(df$taxid)) {
-        stop('The dataframe must at least contain a "taxid" column')
-    }
-    # create a new "environment" to store the full data
-    if(!exists("lifemap_basemap_envir", where = .GlobalEnv)) lifemap_basemap_envir <- new.env()
-
-    ## SET DATASETS ASDRESSES
-    # getting the right URL depending on the basemap wanted
-    if(basemap == "ncbi") {
-        basemap_url <- "https://lifemap-ncbi.univ-lyon1.fr/data/lmdata.Rdata"
-    } else if(basemap == "fr") {
-        basemap_url <- "https://lifemap-fr.univ-lyon1.fr/data/lmdata.Rdata"
-    } else if(basemap == "base") {
-        basemap_url <- "https://lifemap.univ-lyon1.fr/data/lmdata.Rdata"
-    }
-    # else if(basemap == "virus") {
-    #   basemap_url <- "https://virusmap.univ-lyon1.fr/data/lmdata.Rdata"
-    # }
-    else {
-        stop(sprintf('%s is not a working basemap, try c("base", "fr", "ncbi" or "virus")', basemap))
-    }
-
-    # download full data for chosen basemap
-    if(verbose) cat("Downloading basemap coordinates...\n")
-
-    # control to test if the url is valid
-    if(!url.exists(basemap_url)) stop ("The Lifemap server or some remote lifemap files cannot be reached. Please try again later.")
+
+  basemap <- match.arg(arg = basemap, choices = basemap)
+  if(is.null(df$taxid)) {
+    stop('The dataframe must at least contain a "taxid" column')
+  }
+  # create a new "environment" to store the full data
+  if(!exists("lifemap_basemap_envir", where = .GlobalEnv)) lifemap_basemap_envir <- new.env()
+
+  ## SET DATASETS ASDRESSES
+  # getting the right URL depending on the basemap wanted
+  if(basemap == "ncbi") {
+    basemap_url <- "https://lifemap-ncbi.univ-lyon1.fr/data/lmdata.Rdata"
+  } else if(basemap == "fr") {
+    basemap_url <- "https://lifemap-fr.univ-lyon1.fr/data/lmdata.Rdata"
+  } else if(basemap == "base") {
+    basemap_url <- "https://lifemap.univ-lyon1.fr/data/lmdata.Rdata"
+  }
+  # else if(basemap == "virus") {
+  #   basemap_url <- "https://virusmap.univ-lyon1.fr/data/lmdata.Rdata"
+  # }
+  else {
+    stop(sprintf('%s is not a working basemap, try c("base", "fr", "ncbi" or "virus")', basemap))
+  }
+
+  # download full data for chosen basemap
+  if(verbose) cat("Downloading basemap coordinates...\n")
+
+  # control to test if the url is valid
+  if(!url.exists(basemap_url)) {
+    message("The Lifemap server or some remote lifemap files cannot be reached. Please try again later.")
+  } else {
     load(url(basemap_url), envir = lifemap_basemap_envir)
 
     # add LUCA
@@ -109,4 +111,5 @@ build_Lifemap <- function(df, basemap = c("ncbi", "base", "fr", "virus"), verbos
     class(lm_obj) <- c("lifemap_obj", "list")
 
     return(lm_obj)
+  }
 }

R/display_map.R

@@ -29,8 +29,11 @@ display_map <- function(df = NULL,basemap = c("fr","ncbi", "base","virus")) {
     display="https://virusmap.univ-lyon1.fr/osm_tiles/{z}/{x}/{y}.png"
   }
   url2check<-strsplit(display, "osm_tiles")[[1]][1]
-  if (!url.exists(url2check)) stop ("The Lifemap server or some remote lifemap files cannot be reached. Please try again later.")
-  m <- leaflet::leaflet(df) |>
-    leaflet::addTiles(display, options = leaflet::providerTileOptions(minZoom = 5, maxZoom = 50))
-  return(m)
+  if (!url.exists(url2check)) {
+    message("The Lifemap server or some remote lifemap files cannot be reached. Please try again later.")
+  } else {
+    m <- leaflet::leaflet(df) |>
+      leaflet::addTiles(display, options = leaflet::providerTileOptions(minZoom = 5, maxZoom = 50))
+    return(m)
+  }
 }

vignettes/runLifemapR.Rmd

@@ -48,14 +48,15 @@ require("LifemapR")
 The very first step to use this package is to have a dataframe containing at least a ```taxid``` column containing NCBI format TaxIds. This dataframe can also contain other data that you might want to visualise.
 
 ```{r echo = FALSE, results=FALSE, warning=FALSE}
-require("LifemapR")
+require("LifemapR", quietly = TRUE)
 
 data(eukaryotes_1000)
 LM_eukaryotes <- build_Lifemap(eukaryotes_1000, "ncbi")
 ```
 
 ```{r echo = FALSE}
-LM_eukaryotes$df[6:10,1:5]
+if(is.lifemap_obj(LM_eukaryotes))
+  LM_eukaryotes$df[6:10,1:5]
 ```
 
 You can then transform this dataframe into a format suitable for the visualisation functions of the package with the ```build_Lifemap``` function.\