gganim: gganim

In tdhock/gganim: Convert ggplots to animations

Description

Convert a ggplot to an animation.

Usage

gganim(anim)

Arguments

anim	ggplot containing time aesthetic. Individual values of the time aesthetic will be used for each frame of the animation.

Author(s)

Toby Dylan Hocking

Examples

library(nicholsonppp)
a <- sim.drift.selection(s=0.1)
dimnames(a$simulated.freqs) <-
  list("locus"=NULL,"population"=NULL,"generation"=NULL)
library(reshape2)
freq <- melt(a$sim)


sorted.s <- a$s[with(a$s,order(S,ancestral)),]
sorted.s$sorted.id <- 1:nrow(sorted.s)
sorted.s <- sorted.s[order(sorted.s$locus),]

loc.pop.colors <- as.matrix(sorted.s[,grepl("color",names(sorted.s))])
dimnames(loc.pop.colors) <- list(locus=NULL,population=NULL)
colors.df <- melt(loc.pop.colors)

## quick merge and check
test <- data.frame(freq,colors.df)
with(test,sum(locus!=locus.1))
with(test,sum(population!=population.1))
merged <- with(test,{
  data.frame(locus,population,generation,value,
             color=value.1,
             sorted.id=sorted.s$sorted.id)
})

## freq vs time plot
l.id <- subset(a$s,type=="positive")$locus[1]
l1 <- subset(merged,locus==l.id)
color.key <- c(blue="blue",red="red",neutral="turquoise")
library(ggplot2)
ggplot(l1,aes(generation,value))+
  geom_line(aes(group=population,colour=color))+
  scale_colour_manual(values=color.key)+
  opts(title=with(a$s[l.id,],sprintf("locus %d s=%f selection=%s",
             l.id,s,type)))

## freq dotplot for 1 generation
g1 <- subset(merged,generation==50)
ggplot(g1,aes(sorted.id,value))+
  geom_point(aes(y=ancestral),data=sorted.s,pch=21)+
  geom_point(aes(colour=color))+
  scale_colour_manual(values=color.key)+
  ylim(0,1)+
  ylab("blue allele frequency")

## animation
anim <- ggplot(,aes(sorted.id))+
  geom_point(aes(y=ancestral),data=sorted.s,pch=21)+
  geom_point(aes(y=value,colour=color,time=generation),data=merged)+
  scale_colour_manual(values=color.key)+
  ylim(0,1)+
  ylab("blue allele frequency")

print(anim) ## this ignores the time aesthetic
library(animation)
saveHTML({
  gganim(anim)
})

tdhock/gganim documentation built on May 31, 2019, 7:36 a.m.