sábado, 9 de diciembre de 2017

Brownian Motion GIF with R and ImageMagick



Hi there!

Last Monday we celebrated a “Scientific Marathon” at Royal Botanic Garden in Madrid, a kind of mini-conference to talk about our research. I was talking about the relation between fungal spore size and environmental variables such as temperature and precipitation. To make my presentation more friendly, I created a GIF to explain the Brownian Motion model. In evolutionary biology, we can use this model to simulate the random variation of a continuous trait through time. Under this model, we can notice how closer species tend to maintain closer trait values due to shared evolutionary history. You have a lot of information about Brownian Motion models in evolutionary biology everywhere!
Here I will show you how I built a GIF to explain Brownian Motion in my talk using R and ImageMagick.


 # First, we simulate continuous trait evolution by adding in each iteration  
 # a random number from a normal distribution with mean equal to 0 and standard  
 # deviation equal to 1. We simulate a total of 4 processes, to obtain at first  
 # two species and a specieation event at the middle of the simulation, obtaining  
 # a total of 3 species at the end.  
 df1<- data.frame(0,0)  
 names(df1)<- c("Y","X")  
 y<-0  
 for (g in 1:750){  
 df1[g,2] <- g  
 df1[g,1] <- y  
 y <- y + rnorm(1,0,1)  
 }  
 #plot(df1$X,df1$Y, ylim=c(-100,100), xlim=c(0,1500), cex=0)  
 #lines(df1$X,df1$Y, col="red")  
 df2<- data.frame(0,0)  
 names(df2)<- c("Y","X")  
 y<-0  
 for (g in 1:1500){  
  df2[g,2] <- g  
  df2[g,1] <- y  
  y <- y + rnorm(1,0,1)  
 }  
 #lines(df2$X,df2$Y, col="blue")  
 df3<- data.frame(750,df1[750,1])  
 names(df3)<- c("Y","X")  
 y<-df1[750,1]  
 for (g in 750:1500){  
  df3[g-749,2] <- g  
  df3[g-749,1] <- y  
  y <- y + rnorm(1,0,1)  
 }  
 #lines(df3$X,df3$Y, col="green")  
 df4<- data.frame(750,df1[750,1])  
 names(df4)<- c("Y","X")  
 y<-df1[750,1]  
 for (g in 750:1500){  
  df4[g-749,2] <- g  
  df4[g-749,1] <- y  
  y <- y + rnorm(1,0,1)  
 }  
 #lines(df4$X,df4$Y, col="orange")  



 # Now, we have to plot each simmulation lapse and store them in our computer.  
 # I added some code to make lighter the gif (plotting just odd generations) and   
 # to add a label at the speciation time. Note that, since Brownan Model is a   
 # stocasthic process, my simulation will be different from yours.  
 # You should adjust labels or repeat the simulation process if you don't   
 # like the shape of your plot.  
 parp<-rep(0:1, times=7, each= 15)  
 parp<- c(parp, rep(0, 600))  
 for (q in 1:750){  
  if ( q %% 2 == 1) {  
  id <- sprintf("%04d", q+749)  
  png(paste("bm",id,".png", sep=""), width=900, height=570, units="px",   
    pointsize=18)  
  par(omd = c(.05, 1, .05, 1))  
  plot(df1$X,df1$Y, ylim=c(-70,70), xlim=c(0,1500), cex=0,   
     main=paste("Brownian motion model \n generation=", 749 + q) ,   
     xlab="generations", ylab="trait value", font.lab=2, cex.lab=1.5 )  
 lines(df1$X,df1$Y, col="red", lwd=4)  
 lines(df2$X[1:(q+749)],df2$Y[1:(q+749)], col="blue", lwd=4)  
 lines(df3$X[1:q],df3$Y[1:q], col="green", lwd=4)  
 lines(df4$X[1:q],df4$Y[1:q], col="orange", lwd=4)  
 if (parp[q]==0)  
 text(750, 65,labels="speciation event", cex= 1.5, col="black", font=2)  
 if (parp[q]==0)  
 arrows(750, 60, 750, 35, length = 0.20, angle = 30, lwd = 3)  
 dev.off()  
 }  
 }  

 Now, you just have to use ImageMagick to put all the PNG files together in a GIF using a command like this in a terminal:


 convert -delay 10 *.png bm.gif  

Et voilà!



2 comentarios:

  1. Nice post! Alternatively you can use the magick package(https://cran.r-project.org/web/packages/magick/index.html) to create the animated plot directly in R using something like:

    library(tidyverse)
    library(magick)
    list.files(pattern = "png") %>% image_read() %>% image_animate(fps=10) %>% image_write("bm.gif")

    ResponderEliminar
    Respuestas
    1. Hi Paolo!

      Thanks so much for the advice! I didn't know the "magick" package, looks pretty cool!
      Cheers

      Eliminar