script for plotting mammal research data

newMammals.R

library(ggplot2)
library(dplyr)
library(gridExtra)
library(rphylopic)

MammalDisc <- read.csv(file = "https://raw.githubusercontent.com/luisDVA/codeluis/master/mammalDiscoveries.csv",stringsAsFactors = FALSE)

# plot search results by order for all orders
ggplot(MammalDisc,aes(results,reorder(sp,descYear)))+
  geom_point() + theme_minimal() + theme(axis.text.y = element_blank())+
  facet_wrap( ~ order,scales = "free", ncol=2)+ylab("species")

# plot search results for entire dataset
ggplot(MammalDisc,aes(descYear,results))+geom_point(pch=21,size=4,position = "jitter")+
  theme_minimal()+xlab("description year")+ylab("number of search results")

# plot search results by order for orders with >2 new species
MammalDisc %>% group_by(order) %>% mutate(count=n()) %>% 
  filter(count>2) %>% 
  ggplot(aes(results,reorder(sp,descYear)))+
  geom_point() + theme_minimal() + theme(axis.text.y = element_blank())+
  facet_wrap( ~ order,scales = "free", ncol=2)+ylab("species")

# plots for Rodentia and Chiroptera

# get background imaged from Phylopic
imgRat <- image_data("0f6af3d8-49d2-4d75-8edf-08598387afde", size = "512")[[1]]
imgBat <- image_data("18bfd2fc-f184-4c3a-b511-796aafcc70f6", size = "512")[[1]]

# create plot objects

ratPlot <- MammalDisc %>% filter(order=="Rodentia") %>% 
  ggplot(aes(results,reorder(sp,descYear)))+
  geom_text(aes(label=descYear))+
  theme_minimal()+
  add_phylopic(imgRat) +xlab("")+ylab("")

batPlot <- MammalDisc %>% filter(order=="Chiroptera") %>% 
  ggplot(aes(results,reorder(sp,descYear)))+
  geom_text(aes(label=descYear))+
  theme_minimal()+
  add_phylopic(imgBat)+xlab("")+ylab("")

# plot side by side

grid.arrange(ratPlot, batPlot, ncol=2, 
             bottom="Google Scholar hits",
             left= "species",widths=c(1,1))