Update make_maps.R

code/make_maps.R

@@ -24,13 +24,15 @@ class(coord)
 
 # Whole dataset map
 qmplot(lon,lat,data=coord,maptype="stamen_toner_lite",color=I("red"))
+# OR
+ggmap(Med_map)+geom_point(data=coord,aes(color="darkred",shape=Age))
 ggsave("dataset_map.pdf",width=9,height=5) 
 
 # Color by stage
 Tortonian<-filter(coord,Age=="Tortonian")
 Messinian<-filter(coord,Age=="pre-evaporitic Messinian")
 Zanclean<-filter(coord,Age=="Zanclean")
-ggmap(Med_map)+geom_point(data=Tortonian,color="blue")+geom_point(data=Messinian,color="red")+geom_point(data=Zanclean,color="yellow")
+ggmap(Med_map)+geom_point(data=Tortonian,color="darkblue")+geom_point(data=Messinian,color="darkred")+geom_point(data=Zanclean,color="gold2")
 ggsave("locs_by_stage_map.pdf",width=9,height=5)
 
 # Color by region
@@ -48,4 +50,76 @@ ggmap(Med_map)+
   labs(x="longitude",y="latitude")+
   theme(legend.position="bottom")
 
-ggsave("stage_region_map2.pdf",width=9,height=5)
+ggsave("stage_region_map2.pdf",width=9,height=5)
+
+# plot for each group separately
+tax_groups<-unique(coord$group.name)
+pforams<-filter(coord,group.name=="planktic_foraminifera")
+nano<-filter(coord,group.name=="nanoplankton")
+ostracods<-filter(coord,group.name=="ostracods")
+bforams<-filter(coord,group.name=="benthic_foraminifera")
+gastr<-filter(coord,group.name=="gastropods")
+echinoids<-filter(coord,group.name=="echinoids")
+fish<-filter(coord,group.name=="fish")
+mmammals<-filter(coord, group.name=="marine_mammals")
+biv<-filter(coord,group.name=="bivalves")
+corals<-filter(coord,group.name=="corals")
+dino<-filter(coord,group.name=="dinocysts")
+sharks<-filter(coord,group.name=="sharks")
+bryo<-filter(coord,group.name=="bryozoans")
+othermolluscs<-filter(coord, group.name=="scaphopod_chitons_cephalopods")
+
+ggmap(Med_map)+geom_point(data=pforams,aes(color=Age))
+ggsave("pforams.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=nano,aes(color=Age))
+ggsave("nano.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=ostracods,aes(color=Age))
+ggsave("ostracods.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=bforams,aes(color=Age))
+ggsave("bforams.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=gastr,aes(color=Age))
+ggsave("gastro.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=echinoids,aes(color=Age))
+ggsave("echinoids.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=fish,aes(color=Age))
+ggsave("fish.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=mmammals,aes(color=Age))
+ggsave("marine_mammals.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=biv,aes(color=Age))
+ggsave("bivalves.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=corals,aes(color=Age))
+ggsave("corals.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=dino,aes(color=Age))
+ggsave("dino.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=sharks,aes(color=Age))
+ggsave("sharks.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=bryo,aes(color=Age))
+ggsave("bryo.pdf",width=9,height=5)
+
+ggmap(Med_map)+geom_point(data=othermolluscs,aes(color=Age))
+ggsave("othermolluscs.pdf",width=9,height=5)
+
+# plot groups split into plankton, benthos, necton and large marine vertebrates
+# plankton: planktic_foraminifera, nanoplankton, dinocysts
+# benthos: benthic_foraminifera, bryozoans, molluscs, echinoids, corals
+# necton: fish, ostracods 
+# large marine vertebrates: sharks, marine mammals
+plankton<-rbind(pforams,nano,dino)
+benthos<-rbind(bforams,bryo,othermolluscs,gastr,biv,echinoids,corals)
+necton<-rbind(fish,ostracods)
+large_mar_vert<-rbind(sharks,mmammals)
+
+ggmap(Med_map)+geom_point(data=plankton,color="gold1",aes(shape=Age))+geom_point(data=benthos,color="red",aes(shape=Age))+geom_point(data=necton,color="blue",aes(shape=Age))+geom_point(data=large_mar_vert,color="green",aes(shape=Age))
+ggsave("fgroups.pdf",width=9,height=5)