diff Map_shp.R @ 0:ce9979488ebb draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Map_shp.R	Sat Nov 25 15:18:33 2023 +0000
@@ -0,0 +1,62 @@
+library(ggplot2)
+library(sf)
+library(dplyr)
+library(RColorBrewer)
+library(ggspatial)
+
+args = commandArgs(trailingOnly=TRUE) 
+if (length(args)==0)
+{
+    stop("This tool needs at least one argument")
+}else{
+    dataMap <- args[1]
+    dataEvo <- args[2]
+    title <- args[3]
+    legend <- args[4]
+    coord <- args[5]
+     
+}
+
+title <- gsub("\\\\n", "\n", title) 
+legend <-gsub("\\\\n", "\n", legend) 
+#read data
+
+data_map = st_read(dataMap)
+data_evo = read.delim(dataEvo,header=TRUE,sep="\t")
+
+#bring together data
+
+data_fin = bind_cols(data_map,data_evo[2])
+
+
+# define the data intervals
+intervals <- cut(data_fin$Evolution_rate, breaks = c(-Inf, 0, 9, 20, Inf), labels = c("Moins de 0", "0 à 10", "10 à 20", "Plus de 20"))
+
+# Make the map with ggplot2 
+
+if (coord == "true"){
+  ggplot(data_fin) +
+    geom_sf(aes(fill = intervals)) +
+    scale_fill_manual(values = c('#D9F0D3',"#A6DBA0","#5AAE61","#1B7837")) +
+    labs(title = title, fill = legend) +
+    annotation_scale()
+    
+  #outuput 
+  ggsave("map.pdf", device = "pdf")
+
+}else{
+  ggplot(data_fin) +
+    geom_sf(aes(fill = intervals)) +
+    scale_fill_manual(values = c('#D9F0D3',"#A6DBA0","#5AAE61","#1B7837")) +
+    labs(title = title, fill = legend) +
+    theme_void()+
+    annotation_scale()
+    
+  #outuput 
+  ggsave("map.pdf", device = "pdf")
+}
+
+
+
+
+