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plot_BF_2.R
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plot_BF_2.R
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#by Sebastian Hoehna
#trace.size()
#pp_Porifera
#pp_Ctenophora
#pp_Cnidaria
#pp_Xenacoelomorpha
#pp_Hemichordata
#pp_Echinodermata
#pp_Lophotrochozoa
#pp_Ecdysozoa
#pp_metazoans
#pp_metazoans_ingroup
#pp_Ctenophora_Sister
#pp_Porifera_Sister
#pp_Deuterostome
#pp_Nephrozoa
#pp_Xenambulacraria
library(ggplot2)
library(gridExtra)
library(egg)
compute.BF <- function( pp1, pp2, n.samples ) {
# modify pp1 and pp2 so that we exclude the boundaries
pp1 <- ifelse( pp1 == 1.0, pp1-(1/n.samples), ifelse( pp1 == 0, pp1+(1/n.samples), pp1 ) )
pp2 <- ifelse( pp2 == 1.0, pp2-(1/n.samples), ifelse( pp2 == 0, pp2+(1/n.samples), pp2 ) )
# brute force BF
BF <- pp1 / pp2
ln.bf <- log( BF )
return (ln.bf)
}
compute.prior <- function( focal.clade.size, total.n.species ) {
ln_total_prior <- 0
if ( (total.n.species-focal.clade.size+1) > 2 ) {
for (i in 3:(total.n.species-focal.clade.size+1) ) {
ln_total_prior <- ln_total_prior - log(2*i-3)
}
}
if ( focal.clade.size > 2 ) {
for (i in 3:focal.clade.size ) {
ln_total_prior <- ln_total_prior - log(2*i-3)
}
}
return (ln_total_prior)
}
METHODS = c( "Homogroups","Orthogroups")
I_VALUES = c( "1.5", "2", "2.5", "4", "6" )
E_VALUES = c( "1e-2", "1e-5", "1e-9", "1e-12")
N_RUNS = 4
NUM_SPECIES_THIS_DATASET = 47
pp <- as.data.frame( list(method=c(),i_val=c(),e_val=c(),rep=c(),n_samples=c()) )
method = c()
i_val = c()
e_val = c()
rep = c()
n_samples = c()
pp_Porifera = c()
pp_Ctenophora = c()
pp_Cnidaria = c()
pp_Xenacoelomorpha = c()
pp_Hemichordata = c()
pp_Echinodermata = c()
pp_Lophotrochozoa = c()
pp_Ecdysozoa = c()
pp_metazoans = c()
pp_metazoans_ingroup = c()
pp_Ctenophora_Sister = c()
pp_Porifera_Sister = c()
pp_Deuterostome = c()
pp_Nephrozoa = c()
pp_Xenambulacraria = c()
bf_Porifera = c()
bf_Xenacoelomorpha = c()
bf_Deutorostome = c()
for ( m in METHODS ) {
for ( iv in I_VALUES ) {
for ( ev in E_VALUES ) {
for ( r in 1:N_RUNS ) {
filename <- paste0("47sp_metazoan_hypothesis/",m,"_",ev,"_",iv,"_run_",r,".txt")
if ( file.exists(filename) == FALSE ) cat(filename,"does not exist.\n")
this.pp = read.csv(filename, header=FALSE)[,1]
method = append(method,m)
i_val = append(i_val,iv)
e_val = append(e_val,ev)
rep = append(rep,r)
n_samples = append(n_samples, this.pp[1])
pp_Porifera = append(pp_Porifera, this.pp[2])
pp_Ctenophora = append(pp_Ctenophora, this.pp[3])
pp_Cnidaria = append(pp_Cnidaria, this.pp[4])
pp_Xenacoelomorpha = append(pp_Xenacoelomorpha, this.pp[5])
pp_Hemichordata = append(pp_Hemichordata, this.pp[6])
pp_Echinodermata = append(pp_Echinodermata, this.pp[7])
pp_Lophotrochozoa = append(pp_Lophotrochozoa, this.pp[8])
pp_Ecdysozoa = append(pp_Ecdysozoa, this.pp[9])
pp_metazoans = append(pp_metazoans, this.pp[10])
pp_metazoans_ingroup = append(pp_metazoans_ingroup, this.pp[11])
pp_Ctenophora_Sister = append(pp_Ctenophora_Sister, this.pp[12])
pp_Porifera_Sister = append(pp_Porifera_Sister, this.pp[13])
pp_Deuterostome = append(pp_Deuterostome, this.pp[14])
pp_Nephrozoa = append(pp_Nephrozoa, this.pp[15])
pp_Xenambulacraria = append(pp_Xenambulacraria, this.pp[16])
bf_Porifera = append(bf_Porifera,compute.BF(this.pp[13],this.pp[12],this.pp[1])+compute.prior(33,NUM_SPECIES_THIS_DATASET)-compute.prior(35,NUM_SPECIES_THIS_DATASET))
bf_Xenacoelomorpha = append(bf_Xenacoelomorpha,compute.BF(this.pp[15],this.pp[16],this.pp[1])+compute.prior(10,NUM_SPECIES_THIS_DATASET)-compute.prior(22,NUM_SPECIES_THIS_DATASET))
bf_Deutorostome = append(bf_Deutorostome,compute.BF(this.pp[14],1-this.pp[14],this.pp[1])+compute.prior(11,NUM_SPECIES_THIS_DATASET)-compute.prior(11,NUM_SPECIES_THIS_DATASET))
}
}
}
}
pp <- as.data.frame( list(method = method,
i_val = i_val,
e_val = e_val,
rep = as.factor(rep),
n_samples = n_samples,
pp_Porifera = pp_Porifera,
pp_Ctenophora = pp_Ctenophora,
pp_Cnidaria = pp_Cnidaria,
pp_Xenacoelomorpha = pp_Xenacoelomorpha,
pp_Hemichordata = pp_Hemichordata,
pp_Echinodermata = pp_Echinodermata,
pp_Lophotrochozoa = pp_Lophotrochozoa,
pp_Ecdysozoa = pp_Ecdysozoa,
pp_metazoans = pp_metazoans,
pp_metazoans_ingroup = pp_metazoans_ingroup,
pp_Ctenophora_Sister = pp_Ctenophora_Sister,
pp_Porifera_Sister = pp_Porifera_Sister,
pp_Deuterostome = pp_Deuterostome,
pp_Nephrozoa = pp_Nephrozoa,
pp_Xenambulacraria = pp_Xenambulacraria,
bf_Porifera = bf_Porifera,
bf_Xenacoelomorpha = bf_Xenacoelomorpha,
bf_Deutorostome = bf_Deutorostome ) )
write.csv(pp, "Results.csv")
HYPOTHESIS = c("bf_Porifera", "bf_Xenacoelomorpha", "bf_Deutorostome")
for ( m in METHODS ) {
for ( h in HYPOTHESIS ) {
plot_list <- list()
plot_index <- 1
for ( iv in I_VALUES ) {
indices <- pp[["method"]] == m & pp[["i_val"]] == iv
this.df <- pp[indices,]
MAX_BF = ceiling( max( abs( pp[[h]] ) ) )
p <- ggplot(this.df, aes_string(x="e_val", y=h, fill="rep")) +
ggtitle(paste0("I = ",iv)) +
ylim(-MAX_BF,MAX_BF) +
geom_bar(stat="identity", position=position_dodge()) +
scale_fill_brewer(type="seq", palette="Greens")
if ( iv == I_VALUES[1] ) {
p <- p + theme(legend.position="none",
panel.background = element_blank(),
panel.border = element_rect(colour = "black", fill=NA, size=1),
plot.title = element_text(hjust = 0.5))
} else {
p <- p + theme(legend.position="none",
panel.background = element_blank(),
panel.border = element_rect(colour = "black", fill=NA, size=1),
axis.ticks.y = element_blank(),
axis.text.y = element_blank(),
axis.title.y = element_blank(),
plot.title = element_text(hjust = 0.5))
}
p <- p +
geom_hline(yintercept=0, linetype="solid", color = "black", size=0.25) +
geom_hline(yintercept=log(3.2), linetype="dotted", color = "red", size=0.25) +
geom_hline(yintercept=-log(3.2), linetype="dotted", color = "red", size=0.25) +
geom_hline(yintercept=log(10), linetype="dashed", color = "red", size=0.25) +
geom_hline(yintercept=-log(10), linetype="dashed", color = "red", size=0.25) +
geom_hline(yintercept=log(100), linetype="solid", color = "red", size=0.25) +
geom_hline(yintercept=-log(100), linetype="solid", color = "red", size=0.25)
plot_list[[plot_index]] <- p
plot_index <- plot_index + 1
}
all.plots = ggarrange(plots=plot_list, nrow = 1)
ggsave( paste0("BF_",m,"_",h,".pdf"), plot=all.plots, width=15, height=3 )
}
}
cat("Finished!\n")