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sleap_behaviorvisualizer.R
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sleap_behaviorvisualizer.R
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## Chase Analysis: Individual Variation
library(rhdf5)
library(here)
library(tidyverse)
library(zoo)
library(reshape2)
library(data.table)
library(zoo)
library(REdaS)
library(ggpubr)
#based on bfd generated in 'behaviorextraction'
#tmp check with a single chase, to make sure everything works:
behaviorlist <- split(bdf, bdf$BehaviorID)
#Big ol figure generator:
behaviorlist <- split(bdf, bdf$BehaviorID)
arrangeplots <- function (n){
p1 = ggplot(n, aes(x=second, y=velocity_mmpersec, group=BehaviorID))+
geom_line()+
theme_classic()+
facet_wrap(~track, ncol=1)
p2 = ggplot(n, aes(x=second, y=acceleration_mmpsps, group=BehaviorID))+
geom_line()+
theme_classic()+
facet_wrap(~track, ncol=1)
p3 = ggplot(n, aes(x=second, y=theta, group=BehaviorID))+
geom_line()+
theme_classic()+
facet_wrap(~track, ncol=1)
p4 = ggplot(n, aes(x=second, y=truenn, fill=truenndist))+
geom_tile()+
theme_classic()+
ylab("Fish Combination")+
xlab("Time (Seconds)")+
labs(fill="Dist Btwn\nFish (mm)")+
theme(text=element_text(size=15),
legend.title = element_text(size=10),
legend.text = element_text(size=8),
legend.position = c(0.95, 0.9),
legend.key.height = unit(0.25, 'cm'),
legend.background = element_rect(fill="transparent"))
p5 = ggplot(n, aes(x=x, y=y, group=as.factor(track), color=as.factor(track)))+
geom_segment(aes(xend=x+vx, yend=y+vy), arrow=arrow(length=unit(0.1, "cm")), linewidth=0.25)+
theme_classic()+
ylab("Vector Y Component")+
xlab("Vector X Component")+
labs(color="Individual")+
theme(text=element_text(size=10),
legend.position = c(0.95, 0.9),
legend.key.height = unit(0.25, 'cm'),
legend.background = element_rect(fill="transparent"))
p6 = ggplot(n)+
geom_histogram(mapping=aes(x=angletofish0, fill="Angle to fish 0"), binwidth=5)+
geom_histogram(mapping=aes(x=angletofish1, fill="Angle to fish 1"), binwidth=5)+
geom_histogram(mapping=aes(x=angletofish2, fill="Angle to fish 2"), binwidth=5)+
geom_histogram(mapping=aes(x=angletofish3, fill="Angle to fish 3"), binwidth=5)+
geom_histogram(mapping=aes(x=angletofish4, fill="Angle to fish 4"), binwidth=5)+
coord_polar()+
theme_bw()+
theme(legend.position = c(0.8, 0.28),
axis.title.x=element_blank(),
axis.title.y=element_blank(),
axis.text.x = element_text(size=8))+
facet_wrap(~track)
finalplot = ggarrange(
ggarrange(p1, p2, p3, p4, ncol=4, labels = c("Velocity (MMPS)", "Acceleration (MMPSPS)", "Tail Angle (Deg)", "Nearest Neighbor Dist (MM)")),
ggarrange(p5, p6, ncol=2, labels =c("Vector Field", "Relative Heading (Deg)")),
nrow=2)
}
arrangedplotlist <- lapply(behaviorlist, arrangeplots)
plotnames <- paste("chase", unique(bdf$BehaviorID), sep='-')
names(arrangedplotlist) <- plotnames
lapply(names(arrangedplotlist),
function(x) ggsave(filename=paste(x,".png",sep=""),
plot=arrangedplotlist[[x]],
width = 50,
height = 60,
unit = "cm",
path=here("Figures")))
###################################################################################
#tmp invidual checks
#idk if I'll use it but this is a really nice palette, for future:
#
# palette <- c("#729ECE", "#6FB899", "#31A1B3", "#CCB22B","#FF9E4A")
#
# #still need to get rid of the 0 bin but other than that this is workable.
# ggplot(chase10)+
# geom_histogram(mapping=aes(x=angletofish0, fill="Angle to fish 0"), binwidth=5)+
# geom_histogram(mapping=aes(x=angletofish1, fill="Angle to fish 1"), binwidth=5)+
# geom_histogram(mapping=aes(x=angletofish2, fill="Angle to fish 2"), binwidth=5)+
# geom_histogram(mapping=aes(x=angletofish3, fill="Angle to fish 3"), binwidth=5)+
# geom_histogram(mapping=aes(x=angletofish4, fill="Angle to fish 4"), binwidth=5)+
# coord_polar()+
# theme_bw()+
# theme(legend.position = c(0.8, 0.28),
# axis.title.x=element_blank(),
# axis.title.y=element_blank(),
# axis.text.x = element_text(size=8))+
# facet_wrap(~track)
#
# #vector field:
# ggplot(chase10, aes(x=x, y=y, group=as.factor(track), color=as.factor(track)))+
# geom_segment(aes(xend=x+vx, yend=y+vy), arrow=arrow(length=unit(0.1, "cm")), linewidth=0.25)+
# theme_classic()+
# ylab("Vector Y Component")+
# xlab("Vector X Component")+
# labs(color="Individual")+
# theme(text=element_text(size=10),
# legend.position = c(0.95, 0.9),
# legend.key.height = unit(0.25, 'cm'),
# legend.background = element_rect(fill="transparent"))
#
# #nearest neighbor:
# ggplot(chase10, aes(x=second, y=truenn, fill=truenndist))+
# geom_tile()+
# theme_classic()+
# ylab("Fish Combination")+
# xlab("Time (Seconds)")+
# labs(fill="Dist Btwn\nFish (mm)")+
# theme(text=element_text(size=15),
# legend.title = element_text(size=10),
# legend.text = element_text(size=8),
# legend.position = c(0.95, 0.9),
# legend.key.height = unit(0.25, 'cm'),
# legend.background = element_rect(fill="transparent"))