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Lifemap-ToL · Jul 31, 2024 · 563a6d1 · 563a6d1
1 parent 42a5a84
commit 563a6d1
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Showing 2 changed files with 29 additions and 21 deletions.
diff --git a/R/build_Lifemap.R b/R/build_Lifemap.R
@@ -36,19 +36,21 @@
 build_Lifemap <- function(df, basemap = c("ncbi", "base", "fr", "virus"), verbose = TRUE) {
 
   basemap <- match.arg(arg = basemap, choices = basemap)
-  if(is.null(df$taxid)) {
+  if (is.null(df$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()
+  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") {
+  if (basemap == "ncbi") {
     basemap_url <- "https://lifemap-ncbi.univ-lyon1.fr/data/lmdata.Rdata"
-  } else if(basemap == "fr") {
+  } else if (basemap == "fr") {
     basemap_url <- "https://lifemap-fr.univ-lyon1.fr/data/lmdata.Rdata"
-  } else if(basemap == "base") {
+  } else if (basemap == "base") {
     basemap_url <- "https://lifemap.univ-lyon1.fr/data/lmdata.Rdata"
   }
   # else if(basemap == "virus") {
@@ -71,9 +73,11 @@ build_Lifemap <- function(df, basemap = c("ncbi", "base", "fr", "virus"), verbos
   }
   )
 
-  if(!is.na(y)) {
+  if (!is.na(y)) {
     # download full data for chosen basemap
-    if(verbose) cat("Downloading basemap coordinates...\n")
+    if (verbose) {
+      cat("Downloading basemap coordinates...\n")
+    }
     load(url(basemap_url), envir = lifemap_basemap_envir)
 
     # add LUCA
@@ -82,17 +86,21 @@ build_Lifemap <- function(df, basemap = c("ncbi", "base", "fr", "virus"), verbos
 
     # get info for unique taxids (then we work with df_distinct, not df anymore)
     df_distinct <- dplyr::distinct(df, .data$taxid, .keep_all = TRUE)
-    if(nrow(df_distinct) != nrow(df)) {
-        warning(sprintf("%s duplicated TaxIDs were removed \n",nrow(df)-nrow(df_distinct)))
+    if (nrow(df_distinct) != nrow(df)) {
+        warning(sprintf("%s duplicated TaxIDs were removed \n", nrow(df) - nrow(df_distinct)))
     }
 
     # get data
-    if(verbose) cat("Getting info for requested taxids...\n")
+    if (verbose) {
+      cat("Getting info for requested taxids...\n")
+    }
 
     # get index of requested taxids
     indexes <- fastmatch::fmatch(df_distinct$taxid, lifemap_basemap_envir$DF$taxid)
-    if(sum(is.na(indexes)) > 0) {
-        warning(sprintf("%s TaxID(s) could not be found: %s \n",sum(is.na(indexes)), paste(df_distinct$taxid[is.na(indexes)], sep=",")))
+    if (sum(is.na(indexes)) > 0) {
+        warning(sprintf("%s TaxID(s) could not be found: %s \n",
+                        sum(is.na(indexes)), 
+                        paste(df_distinct$taxid[is.na(indexes)], sep = ",")))
     }
 
     # create new df with only existing taxids
@@ -105,8 +113,8 @@ build_Lifemap <- function(df, basemap = c("ncbi", "base", "fr", "virus"), verbos
     ANCESTORS <- lifemap_basemap_envir$DF[fastmatch::fmatch(real_ancestors, lifemap_basemap_envir$DF$taxid), ]
 
     # add type
-    DATA0$type<-"requested"
-    ANCESTORS$type<-"ancestor"
+    DATA0$type <- "requested"
+    ANCESTORS$type <- "ancestor"
     # bind all
     DATA1 <- rbind(DATA0, ANCESTORS)
 

diff --git a/R/display_map.R b/R/display_map.R
@@ -17,18 +17,18 @@
 #'
 #' @examples
 #' display_map()
-display_map <- function(df = NULL, basemap = c("fr","ncbi", "base","virus")) {
+display_map <- function(df = NULL, basemap = c("fr", "ncbi", "base", "virus")) {
   basemap <- match.arg(basemap)
   if (basemap == "fr"){
-    display="http://lifemap-fr.univ-lyon1.fr/osm_tiles/{z}/{x}/{y}.png"
+    display <- "http://lifemap-fr.univ-lyon1.fr/osm_tiles/{z}/{x}/{y}.png"
   } else if (basemap == "ncbi"){
-    display="http://lifemap-ncbi.univ-lyon1.fr/osm_tiles/{z}/{x}/{y}.png"
+    display <- "http://lifemap-ncbi.univ-lyon1.fr/osm_tiles/{z}/{x}/{y}.png"
   } else if (basemap == "base"){
-    display="http://lifemap.univ-lyon1.fr/osm_tiles/{z}/{x}/{y}.png"
+    display <- "http://lifemap.univ-lyon1.fr/osm_tiles/{z}/{x}/{y}.png"
   } else if (basemap == "virus"){
-    display="https://virusmap.univ-lyon1.fr/osm_tiles/{z}/{x}/{y}.png"
+    display <- "https://virusmap.univ-lyon1.fr/osm_tiles/{z}/{x}/{y}.png"
   }
-  url2check<-strsplit(display, "osm_tiles")[[1]][1]
+  url2check <- strsplit(display, "osm_tiles")[[1]][1]
 
   m <- tryCatch({
     leaflet::leaflet(df) |>
@@ -44,7 +44,7 @@ display_map <- function(df = NULL, basemap = c("fr","ncbi", "base","virus")) {
   }
   )
 
-  if(!all(is.na(m))) {
+  if (!all(is.na(m))) {
     return(m)
   } else {
     return(NA)