R/figTests.R
In wgough/LungeKinematics: Kinematics and Energetics of Rorqual Whale Lunges
## Test Figures To Figure Out Energy In Flatline Relationship
pal <- c("Minke" = "#009E73", "Humpback" = "#D55E00", "Blue" = "#0072B2", "Fin" = "#9100B2", "Antarctic" = "Black", "Monterey" = "Gray")
p1 <- ggplot(filter(LungeKinematics::AllWhalesAvgs,Species=="Blue")) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnCostkJ)),
color = "black",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnPerLunge)),
color = "black",
linetype = 2,
se = TRUE) +
geom_point(aes(log10(meanTotLength), log10(meanEnCostkJ), fill = meanJawAreaDirectMeasure),
color = "black",
shape = 21,
size = 10) +
geom_point(aes(log10(meanTotLength), log10(meanEnPerLunge), fill = meanJawAreaDirectMeasure),
color = "black",
shape = 22,
size = 10) +
ggtitle("Jaw Area") +
scale_fill_gradient(low = "blue", high = "red") +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
p2 <- ggplot(filter(LungeKinematics::AllWhalesAvgs,Species=="Blue")) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnCostkJ)),
color = "black",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnPerLunge)),
color = "black",
linetype = 2,
se = TRUE) +
geom_point(aes(log10(meanTotLength), log10(meanEnCostkJ), fill = meanLengthDecel),
color = "black",
shape = 21,
size = 10) +
geom_point(aes(log10(meanTotLength), log10(meanEnPerLunge), fill = meanLengthDecel),
color = "black",
shape = 22,
size = 10) +
ggtitle("Duration of Deceleration") +
scale_fill_gradient(low = "blue", high = "red") +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
p3 <- ggplot(filter(LungeKinematics::AllWhalesAvgs,Species=="Blue")) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnCostkJ)),
color = "black",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnPerLunge)),
color = "black",
linetype = 2,
se = TRUE) +
geom_point(aes(log10(meanTotLength), log10(meanEnCostkJ), fill = meanSpdBegDecel),
color = "black",
shape = 21,
size = 10) +
geom_point(aes(log10(meanTotLength), log10(meanEnPerLunge), fill = meanSpdBegDecel),
color = "black",
shape = 22,
size = 10) +
ggtitle("U Mouth Open") +
scale_fill_gradient(low = "blue", high = "red") +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
p4 <- ggplot(filter(LungeKinematics::AllWhalesAvgs,Species=="Blue")) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnCostkJ)),
color = "black",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnPerLunge)),
color = "black",
linetype = 2,
se = TRUE) +
geom_point(aes(log10(meanTotLength), log10(meanEnCostkJ), fill = meanModelWaterEngulfFull),
color = "black",
shape = 21,
size = 10) +
geom_point(aes(log10(meanTotLength), log10(meanEnPerLunge), fill = meanModelWaterEngulfFull),
color = "black",
shape = 22,
size = 10) +
ggtitle("Water Engulfment Volume") +
scale_fill_gradient(low = "blue", high = "red") +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
p5 <- ggplot(filter(LungeKinematics::AllWhalesAvgs,Species=="Blue")) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnCostkJ)),
color = "black",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnPerLunge)),
color = "black",
linetype = 2,
se = TRUE) +
geom_point(aes(log10(meanTotLength), log10(meanEnCostkJ), fill = meanDecelSpdLoss),
color = "black",
shape = 21,
size = 10) +
geom_point(aes(log10(meanTotLength), log10(meanEnPerLunge), fill = meanDecelSpdLoss),
color = "black",
shape = 22,
size = 10) +
ggtitle("Deceleration Speed Loss") +
scale_fill_gradient(low = "blue", high = "red") +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
p6 <- ggplot(filter(LungeKinematics::AllWhalesAvgs,Species=="Blue")) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnCostkJ)),
color = "black",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnPerLunge)),
color = "black",
linetype = 2,
se = TRUE) +
geom_point(aes(log10(meanTotLength), log10(meanEnCostkJ), fill = meanSlpDecel),
color = "black",
shape = 21,
size = 10) +
geom_point(aes(log10(meanTotLength), log10(meanEnPerLunge), fill = meanSlpDecel),
color = "black",
shape = 22,
size = 10) +
ggtitle("Slope of Deceleration") +
scale_fill_gradient(low = "blue", high = "red") +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
p7 <- cowplot::plot_grid(p1, p2, p3, p4, p5, p6,
nrow = 2,
ncol = 3,
align = "h",
axis = "bl",
labels = NULL)
ggsave("figs/Figure_Test.pdf", height = 960, width = 960, units = "mm", dpi = 300)
SpeedSeriesBlue <- filter(LungeKinematics::SpeedSeries,Species=="Blue")
BlueOnly <- ggplot(SpeedSeriesBlue, aes(secs, Speed)) +
stat_smooth(geom = "line", aes(group = IndNum, color = meanModelWaterEngulfFull),
method = "loess", span = 0.08, size = 2, se = FALSE) +
geom_vline(xintercept = 0) +
scale_color_gradient(low = "blue", high = "red") +
scale_x_continuous(breaks = seq(-10,15,5), limits = c(-10,15)) +
labs(x = "Time (s)",
y = bquote("Swimming Speed (m s"^-1*")")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "none",
panel.grid.minor = element_blank())
ggsave("figs/Figure_Test_2.pdf", height = 480, width = 960, units = "mm", dpi = 300)
ptest3 <- ggplot(LungeKinematics::AllWhalesAvgs) +
geom_point(aes(log10(meanMassSKR), log10(meanEnPerVpos)),
color = "black",
fill = "red",
shape = 21,
size = 10) +
geom_point(aes(log10(meanMassSKR), log10(meanEnPerVant)),
color = "black",
fill = "blue",
shape = 22,
size = 10) +
geom_smooth(method = lm,
aes(log10(meanMassSKR), log10(meanEnPerVpos), group = Species),
color = "red",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanMassSKR), log10(meanEnPerVant), group = Species),
color = "blue",
linetype = 2,
se = TRUE) +
scale_color_manual(values = pal, aesthetics = c("fill","colour")) +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "none",
panel.grid.minor = element_blank())
ptest3
pDepthSpd <- ggplot(LungeKinematics::AllWhalesAvgs) +
geom_smooth(method = lm,
aes(log10(meanDepth), log10(meanSpdBegDecel)),
color = "black",
se = TRUE) +
geom_point(aes(log10(meanDepth), log10(meanSpdBegDecel), fill = Species),
color = "black",
shape = 21,
size = 10) +
labs(x = bquote("Log"^10*" Lunge Depth (m)"),
y = bquote("Log"^10*" Speed Begin Deceleration (m s-1)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
pDepthSpd
wgough/LungeKinematics documentation built on Aug. 6, 2023, 2:08 p.m.
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## Test Figures To Figure Out Energy In Flatline Relationship
pal <- c("Minke" = "#009E73", "Humpback" = "#D55E00", "Blue" = "#0072B2", "Fin" = "#9100B2", "Antarctic" = "Black", "Monterey" = "Gray")
p1 <- ggplot(filter(LungeKinematics::AllWhalesAvgs,Species=="Blue")) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnCostkJ)),
color = "black",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnPerLunge)),
color = "black",
linetype = 2,
se = TRUE) +
geom_point(aes(log10(meanTotLength), log10(meanEnCostkJ), fill = meanJawAreaDirectMeasure),
color = "black",
shape = 21,
size = 10) +
geom_point(aes(log10(meanTotLength), log10(meanEnPerLunge), fill = meanJawAreaDirectMeasure),
color = "black",
shape = 22,
size = 10) +
ggtitle("Jaw Area") +
scale_fill_gradient(low = "blue", high = "red") +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
p2 <- ggplot(filter(LungeKinematics::AllWhalesAvgs,Species=="Blue")) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnCostkJ)),
color = "black",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnPerLunge)),
color = "black",
linetype = 2,
se = TRUE) +
geom_point(aes(log10(meanTotLength), log10(meanEnCostkJ), fill = meanLengthDecel),
color = "black",
shape = 21,
size = 10) +
geom_point(aes(log10(meanTotLength), log10(meanEnPerLunge), fill = meanLengthDecel),
color = "black",
shape = 22,
size = 10) +
ggtitle("Duration of Deceleration") +
scale_fill_gradient(low = "blue", high = "red") +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
p3 <- ggplot(filter(LungeKinematics::AllWhalesAvgs,Species=="Blue")) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnCostkJ)),
color = "black",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnPerLunge)),
color = "black",
linetype = 2,
se = TRUE) +
geom_point(aes(log10(meanTotLength), log10(meanEnCostkJ), fill = meanSpdBegDecel),
color = "black",
shape = 21,
size = 10) +
geom_point(aes(log10(meanTotLength), log10(meanEnPerLunge), fill = meanSpdBegDecel),
color = "black",
shape = 22,
size = 10) +
ggtitle("U Mouth Open") +
scale_fill_gradient(low = "blue", high = "red") +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
p4 <- ggplot(filter(LungeKinematics::AllWhalesAvgs,Species=="Blue")) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnCostkJ)),
color = "black",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnPerLunge)),
color = "black",
linetype = 2,
se = TRUE) +
geom_point(aes(log10(meanTotLength), log10(meanEnCostkJ), fill = meanModelWaterEngulfFull),
color = "black",
shape = 21,
size = 10) +
geom_point(aes(log10(meanTotLength), log10(meanEnPerLunge), fill = meanModelWaterEngulfFull),
color = "black",
shape = 22,
size = 10) +
ggtitle("Water Engulfment Volume") +
scale_fill_gradient(low = "blue", high = "red") +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
p5 <- ggplot(filter(LungeKinematics::AllWhalesAvgs,Species=="Blue")) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnCostkJ)),
color = "black",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnPerLunge)),
color = "black",
linetype = 2,
se = TRUE) +
geom_point(aes(log10(meanTotLength), log10(meanEnCostkJ), fill = meanDecelSpdLoss),
color = "black",
shape = 21,
size = 10) +
geom_point(aes(log10(meanTotLength), log10(meanEnPerLunge), fill = meanDecelSpdLoss),
color = "black",
shape = 22,
size = 10) +
ggtitle("Deceleration Speed Loss") +
scale_fill_gradient(low = "blue", high = "red") +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
p6 <- ggplot(filter(LungeKinematics::AllWhalesAvgs,Species=="Blue")) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnCostkJ)),
color = "black",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanTotLength), log10(meanEnPerLunge)),
color = "black",
linetype = 2,
se = TRUE) +
geom_point(aes(log10(meanTotLength), log10(meanEnCostkJ), fill = meanSlpDecel),
color = "black",
shape = 21,
size = 10) +
geom_point(aes(log10(meanTotLength), log10(meanEnPerLunge), fill = meanSlpDecel),
color = "black",
shape = 22,
size = 10) +
ggtitle("Slope of Deceleration") +
scale_fill_gradient(low = "blue", high = "red") +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
p7 <- cowplot::plot_grid(p1, p2, p3, p4, p5, p6,
nrow = 2,
ncol = 3,
align = "h",
axis = "bl",
labels = NULL)
ggsave("figs/Figure_Test.pdf", height = 960, width = 960, units = "mm", dpi = 300)
SpeedSeriesBlue <- filter(LungeKinematics::SpeedSeries,Species=="Blue")
BlueOnly <- ggplot(SpeedSeriesBlue, aes(secs, Speed)) +
stat_smooth(geom = "line", aes(group = IndNum, color = meanModelWaterEngulfFull),
method = "loess", span = 0.08, size = 2, se = FALSE) +
geom_vline(xintercept = 0) +
scale_color_gradient(low = "blue", high = "red") +
scale_x_continuous(breaks = seq(-10,15,5), limits = c(-10,15)) +
labs(x = "Time (s)",
y = bquote("Swimming Speed (m s"^-1*")")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "none",
panel.grid.minor = element_blank())
ggsave("figs/Figure_Test_2.pdf", height = 480, width = 960, units = "mm", dpi = 300)
ptest3 <- ggplot(LungeKinematics::AllWhalesAvgs) +
geom_point(aes(log10(meanMassSKR), log10(meanEnPerVpos)),
color = "black",
fill = "red",
shape = 21,
size = 10) +
geom_point(aes(log10(meanMassSKR), log10(meanEnPerVant)),
color = "black",
fill = "blue",
shape = 22,
size = 10) +
geom_smooth(method = lm,
aes(log10(meanMassSKR), log10(meanEnPerVpos), group = Species),
color = "red",
se = TRUE) +
geom_smooth(method = lm,
aes(log10(meanMassSKR), log10(meanEnPerVant), group = Species),
color = "blue",
linetype = 2,
se = TRUE) +
scale_color_manual(values = pal, aesthetics = c("fill","colour")) +
labs(x = bquote("Log"^10*" Body Length (m)"),
y = bquote("Log"^10*" Lunge Energy (kJ)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "none",
panel.grid.minor = element_blank())
ptest3
pDepthSpd <- ggplot(LungeKinematics::AllWhalesAvgs) +
geom_smooth(method = lm,
aes(log10(meanDepth), log10(meanSpdBegDecel)),
color = "black",
se = TRUE) +
geom_point(aes(log10(meanDepth), log10(meanSpdBegDecel), fill = Species),
color = "black",
shape = 21,
size = 10) +
labs(x = bquote("Log"^10*" Lunge Depth (m)"),
y = bquote("Log"^10*" Speed Begin Deceleration (m s-1)")) +
theme_classic(base_size = 8) +
theme(axis.text = element_text(size = 30),
axis.title = element_text(size = 36),
legend.position = "right",
legend.title = element_blank(),
panel.grid.minor = element_blank())
pDepthSpd
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