---
tags: Rscripts
---

# Violin plots for dependent variables
### Author: Jocelyn P. Colella
+ These exclude all outliers identified across all DVs (N 430 total, 215 each sex)

## Females

#### daytime

#### nighttime

## Males

#### daytime

#### nighttime

#Function to calculate medians for plotting
data_summary <- function(x) {
  med <- median(x)
  m <- mean(x)
  ymin <- m-sd(x)
  ymax <- m+sd(x)
  return(c(y=med,ymin=ymin,ymax=ymax))
}

#### FEMALE DAYTIME VIOLINE PLOTS
# EE
pEE <- all_day_noOL_F %>%
  ggplot( aes(x=experiment, y=EE, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.title = element_text(size=14)) +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

# RQ
pRQ <- all_day_noOL_F %>%
  ggplot( aes(x=experiment, y=RQ, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  theme(legend.position="none") +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

# VO2
pVO2 <- all_day_noOL_F %>%
  ggplot( aes(x=experiment, y=VO2, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

#VCO2
pVCO2 <- all_day_noOL_F %>%
  ggplot( aes(x=experiment, y=VCO2, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

#H2Omg
pH2O <- all_day_noOL_F %>%
  ggplot( aes(x=experiment, y=H2Omg, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

# PLOT ALL DAYTIME FEMALE PLOTS TOGETHER
plot_grid(pEE, pRQ, pVO2, pVCO2, pH2O,
          labels = c('a) EE', 'b) RQ', 'c) VO2',
                     'd) VCO2', 'e) H2O (mg)'), label_size = 12)



### FEMALE NIGHTTIME VIOLIN PLOTS
# EE
pEE <- all_night_noOL_F %>%
  ggplot( aes(x=experiment, y=EE, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  #geom_dotplot(binaxis='y', stackdir='center', dotsize=0.2, binwidth = 0.01) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.title = element_text(size=14)) +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

# RQ
pRQ <- all_night_noOL_F %>%
  ggplot( aes(x=experiment, y=RQ, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  theme(legend.position="none") +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

# VO2
pVO2 <- all_night_noOL_F %>%
  ggplot( aes(x=experiment, y=VO2, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

#VCO2
pVCO2 <- all_night_noOL_F %>%
  ggplot( aes(x=experiment, y=VCO2, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

#H2Omg
pH2O <- all_night_noOL_F %>%
  ggplot( aes(x=experiment, y=H2Omg, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  #geom_dotplot(binaxis='y', stackdir='center', dotsize=0.2, binwidth = 0.006) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")


# PLOT ALL FEMALE NIGHTITME PLOTS TOGETHER
plot_grid(pEE, pRQ, pVO2, pVCO2, pH2O,
          labels = c('a) EE', 'b) RQ', 'c) VO2',
                     'd) VCO2', 'e) H2O (mg)'),
          label_size = 12)




###################################################
###MALE DAYTIME VIOLIN PLOTS
# EE
pEE <- all_day_noOL_M %>%
  ggplot( aes(x=experiment, y=EE, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.title = element_text(size=14)) +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

# RQ
pRQ <- all_day_noOL_M %>%
  ggplot( aes(x=experiment, y=RQ, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  theme(legend.position="none") +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

# VO2
pVO2 <- all_day_noOL_M %>%
  ggplot( aes(x=experiment, y=VO2, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

#VCO2
pVCO2 <- all_day_noOL_M %>%
  ggplot( aes(x=experiment, y=VCO2, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

#H2Omg
pH2O <- all_day_noOL_M %>%
  ggplot( aes(x=experiment, y=H2Omg, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

# ALL MALE DAYTIME PLOTS TOGETHER
plot_grid(pEE, pRQ, pVO2, pVCO2, pH2O,
          labels = c('a) EE', 'b) RQ', 'c) VO2',
                     'd) VCO2', 'e) H2O (mg)'),
          label_size = 12)




### MALE NIGHT TIME VIOLIN PLOTS
# EE
pEE <- all_night_noOL_M %>%
  ggplot( aes(x=experiment, y=EE, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.title = element_text(size=14)) +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")
pEE 

# RQ
pRQ <- all_night_noOL_M %>%
  ggplot( aes(x=experiment, y=RQ, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  theme(legend.position="none") +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

# VO2
pVO2 <- all_night_noOL_M %>%
  ggplot( aes(x=experiment, y=VO2, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")

#VCO2
pVCO2 <- all_night_noOL_M %>%
  ggplot( aes(x=experiment, y=VCO2, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")
pVCO2

#H2Omg
pH2O <- all_night_noOL_M %>%
  ggplot( aes(x=experiment, y=H2Omg, fill=experiment, color=experiment)) +
  geom_jitter(color = "darkgrey", alpha = 0.5, cex = 0.5) +
  geom_violin(width=1, size=0.5, alpha = 0.8) +
  scale_color_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  scale_fill_manual(values=c("grey31", "#0571B0", "#CA0020")) +
  stat_summary(fun.data=mean_sdl, mult=1, geom="pointrange", color="black") +
  theme_ipsum() +
  theme(legend.position="none") +
  theme(plot.margin = unit(c(0.1,0.1,0.1,0.1), "lines")) +
  theme(plot.title = element_text(size=14)) +
  coord_flip() + # This switch X and Y axis and allows to get the horizontal version
  labs(title="", x = "", y ="")
pH2O


#MALE NIGHTTIME PLOTS TOGETHER
plot_grid(pEE, pRQ, pVO2, pVCO2, pH2O,
          labels = c('a) EE', 'b) RQ', 'c) VO2',
                     'd) VCO2', 'e) H2O (mg)'),
          label_size = 12)