Update ReDU_map_alpha.R

Author: alan-jarmusch

examples/ExtendedDataFigure1/ReDU_map_alpha.R

@@ -21,28 +21,6 @@ chemical_sum <- df_1 %>% group_by(LatitudeandLongitude, Lat, Long, Compound_Name
 chemical_sum <- chemical_sum %>% group_by(LatitudeandLongitude, Lat, Long) %>% summarise(total_hits = sum(Files))
 plot_sum <- chemical_sum %>% left_join(number_files[,c("LatitudeandLongitude","Unique")], by="LatitudeandLongitude") %>% mutate(proportion = total_hits/Unique)
 
-
-
-### PLOT NUMBER OF FILES
-plot_number_files <- subset(number_files, number_files$Lat != "not specified" & number_files$Lat != "not applicable")
-plot_number_files$Unique <- log(plot_number_files$Unique,10)
-#Using GGPLOT, plot the Base World Map
-mp <- NULL
-mapWorld <- borders("world", colour="gray90", fill="gray90") # create a layer of borders
-mp <- ggplot() +  mapWorld 
-print(mp)
-#Now Layer the cities on top
-mp <- mp + geom_point(data=plot_number_files, aes(x=as.numeric(Long), y=as.numeric(Lat), colour=as.numeric(Unique)), size=1.5, alpha=0.7) +
-  scale_color_viridis(option="B")+
-  theme_minimal()+
-  theme(legend.position="bottom",
-        legend.title=element_text(colour="black", size=6),
-        legend.text=element_text(colour="black", size=6))+
-  labs(x="Longitude", y="Latitude", colour = "Log10(# of Files)")
-print(mp)
-#ggsave(mp, file="Manuscript/Figures/Source_Material/ReDU_Map_NumberofFiles.pdf", width = 8, height = 5, units = "in", useDingbats=FALSE)
-
-
 ### PLOT NUMBER OF ANNOTATIONS / FILE
 plot_sum <- subset(plot_sum, plot_sum$Lat != "not specified" & plot_sum$Lat != "not applicable")
 plot_sum$proportion <- log(plot_sum$proportion,10)
@@ -64,8 +42,7 @@ mp <- mp + geom_point(data=plot_sum, aes(x=as.numeric(Long), y=as.numeric(Lat),
         legend.text=element_text(colour="black", size=6))+
   labs(x="Longitude", y="Latitude", colour = "Log10(# of Annotations / # of Files)")
 print(mp)
-ggsave(mp, file="Manuscript/Figures/Source_Material/ReDU_Map_NumberofAnnotationsPerFile.pdf", 
-       width = 3.5, height = 2.5, units = "in", useDingbats=FALSE)
+ggsave(mp, file="Manuscript/Figures/Source_Material/ReDU_Map_NumberofAnnotationsPerFile.pdf", width = 3.5, height = 2.5, units = "in", useDingbats=FALSE)