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Statistical_scripts/Hypo_Graphs.R

+### Script for elife Paper - 18/04/2024
+
+### Install Packages
+
+install.packages("GGally")
+install.packages("ggplot2")       
+install.packages("ggpubr")
+install.packages("readxl")
+install.packages("viridis")
+install.packages("dplyr")
+install.packages("viridis")
+install.packages("plotrix")
+
+### Load Packages
+
+library(viridis)
+library("GGally")
+library("ggplot2")
+library(ggpubr)
+library(readxl)
+library(dplyr)
+library(RColorBrewer)
+library("plotrix")
+
+### Figure 2 - B, C
+
+# Emotinal Task 
+
+E_beta<- read.csv("EMO_hypo_analysis_5areas.csv")
+
+EmoM <- ggplot(E_beta, aes(x=as.factor(Hypo), y=Beta_EDI, fill=as.factor(Emo)))+
+  geom_boxplot()+
+  geom_point(alpha=0.6,position=position_dodge(0.75))+
+  xlab("Hypothalamus Subparts") + 
+  ylab("Betas (a.u.)") + 
+  labs(tag = "C")+
+  labs(fill = "Stimuli")+
+  geom_hline(aes(yintercept=0), colour="azure4", linetype="dashed")+ 
+  theme_classic()+
+  theme(plot.title = element_text(size = 16),text = element_text(size = 24, face="bold"),
+        legend.text = element_text(size = 18, face="bold"), legend.key.size = unit(1, 'cm'),
+        legend.title = element_text(size = 18),
+        legend.position= c(0.7, 0.92), legend.box = "horizontal",
+        legend.background = element_rect(size=0.5, linetype="solid", colour ="black"))+
+  scale_fill_brewer(palette="Purples")
+
+
+### Nback Task
+
+N_beta<- read.csv("Nback_hypo_Analysis_Mel_5areas_Nback.csv")
+
+NbackM <- ggplot(N_beta, aes(x=as.factor(Hypo), y=Beta_EDI_Nback, fill=as.factor(Nback)))+
+  geom_boxplot()+ scale_fill_manual(values=c('#F7FCF5',"#A1D99B"))+
+  geom_point(alpha=0.6,position=position_dodge(0.75))+
+  xlab("Hypothalamus subparts") + 
+  ylab("Betas (a.u.)") + 
+  labs(tag = "B")+
+  labs(fill = "Task")+
+  theme_classic()+
+  theme(plot.title = element_text(size = 16),text = element_text(size = 24, face="bold"),
+        legend.text = element_text(size = 18, face="bold"), legend.key.size = unit(1, 'cm'),
+        legend.title = element_text(size = 18),
+        legend.box = "horizontal", legend.position= c(0.7, 0.92),
+        legend.background = element_rect(size=0.5, linetype="solid", colour ="black"))+
+  geom_hline(aes(yintercept=0), colour="azure4", linetype="dashed")+
+  scale_y_continuous(limits = c(-0.005,0.006))
+
+# Combine Graphs 
+
+ggarrange(NbackM, EmoM, ncol = 2, nrow = 1)
+
+###  Figure 2 - I, J, K, L
+
+### Load executive task data 
+
+Nback2  <- read.csv("Hypothalamus_paper_Nback2_mEDIchange.csv") #mEDI changed from 0.16 to 10 
+
+Nback0  <- read.csv("Hypothalamus_paper_Nback0_mEDIchange.csv") #mEDI changed from 0.16 to 10 
+
+### Load emotional task data 
+
+Emo  <- read.csv("Hypo_5Con_analysis_all_hypo_Emotional_mEDIchange.csv") #mEDI changed from 0.16 to 10 
+
+Neut  <- read.csv("Hypo_5Con_analysis_all_hypo_Neutral_mEDIchange.csv") #mEDI changed from 0.16 to 10 
+
+
+### create graph error bars 
+
+data2 <- Nback2 %>%
+  group_by(Hypo,mEDI)%>%
+  summarise(mean_beta=mean(Beta),se=std.error(Beta),
+            Min=min(Beta),Max=max(Beta), sd=sd(Beta),
+            ci = mean_cl_normal(Beta) %>%
+              rename(mean=y, lwr=ymin, upr=ymax))
+
+data0 <- Nback0 %>%
+  group_by(Hypo,mEDI)%>%
+  summarise(mean_beta=mean(Beta),se=std.error(Beta),
+            Min=min(Beta),Max=max(Beta), sd=sd(Beta),
+            ci = mean_cl_normal(Beta) %>%
+              rename(mean=y, lwr=ymin, upr=ymax))
+
+dataE <- Emo %>%
+  group_by(Hypo,Light)%>%
+  summarise(mean_beta=mean(Betas_Emo),se=std.error(Betas_Emo),
+            Min=min(Betas_Emo),Max=max(Betas_Emo), sd=sd(Betas_Emo),
+            ci = mean_cl_normal(Betas_Emo) %>%
+              rename(mean=y, lwr=ymin, upr=ymax))
+
+dataN <- Neut %>%
+  group_by(Hypo,Light)%>%
+  summarise(mean_beta=mean(Betas_Emo),se=std.error(Betas_Emo),
+            Min=min(Betas_Emo),Max=max(Betas_Emo), sd=sd(Betas_Emo),
+            ci = mean_cl_normal(Betas_Emo) %>%
+              rename(mean=y, lwr=ymin, upr=ymax))
+
+### Create Plots 
+
+# 2-back
+F2I <- ggplot(data2,aes(x=mEDI, y=mean_beta, color=as.factor(Hypo))) +  
+  geom_line(aes(group = Hypo),linewidth =0.8)+
+  scale_color_manual(values=c('#EEEE00','#00008B', "#00F5FF", "#CDB79E", "#00FF00"))+
+  geom_point(alpha=0.6)+
+  xlab("Melanopic EDI") + 
+  ylab("2-back Betas (a.u.)") + 
+  labs(tag = "I")+
+  labs(col = "Hypothalamus Subpart")+
+  theme_classic()+ 
+  theme(text = element_text(size = 16, face="bold"),
+        legend.text = element_text(size = 16, face="bold"), 
+        legend.title = element_text(size = 16),
+        legend.box = "horizontal", legend.position='none')+
+  geom_linerange(aes(ymin=mean_beta-se,ymax=mean_beta+se))+
+  scale_x_continuous(breaks = c(0, 10, 37, 92, 190))
+
+
+# 0-back
+F2J <- ggplot(data0,aes(x=mEDI, y=mean_beta, color=as.factor(Hypo))) +  
+  geom_line(aes(group = Hypo),linewidth =0.8)+
+  scale_color_manual(values=c('#EEEE00','#00008B', "#00F5FF", "#CDB79E", "#00FF00"))+
+  geom_point(alpha=0.6)+
+  xlab("Melanopic EDI") + 
+  ylab("0-back Betas (a.u.)") + 
+  labs(tag = "J")+
+  labs(col = "Hypothalamus Subpart")+
+  theme_classic()+ 
+  theme(text = element_text(size = 16, face="bold"),
+        legend.text = element_text(size = 16, face="bold"), 
+        legend.title = element_text(size = 16),
+        legend.box = "horizontal", legend.position='none')+
+  geom_linerange(aes(ymin=mean_beta-se,ymax=mean_beta+se))+
+  scale_x_continuous(breaks = c(0, 10, 37, 92, 190))
+
+
+
+F2K <- ggplot(dataE,aes(x=Light, y=mean_beta, color=as.factor(Hypo))) +  
+  geom_line(aes(group = Hypo),linewidth =0.8)+
+  scale_color_manual(values=c('#EEEE00','#00008B', "#00F5FF", "#CDB79E", "#00FF00"))+
+  geom_point(alpha=0.6)+
+  xlab("Melanopic EDI") + 
+  ylab("Emotional Betas (a.u.)") + 
+  labs(tag = "K")+
+  labs(col = "Hypothalamus Subpart")+
+  theme_classic()+ 
+  theme(text = element_text(size = 16, face="bold"),
+        legend.text = element_text(size = 16, face="bold"), 
+        legend.title = element_text(size = 16),
+        legend.box = "horizontal", legend.position='none')+
+  geom_linerange(aes(ymin=mean_beta-se,ymax=mean_beta+se))+
+  scale_x_continuous(breaks = c(0, 10, 37, 92, 190))
+
+# Neut
+F2L <- ggplot(dataN,aes(x=Light, y=mean_beta, color=as.factor(Hypo))) +  
+  geom_line(aes(group = Hypo),linewidth =0.8)+
+  scale_color_manual(values=c('#EEEE00','#00008B', "#00F5FF", "#CDB79E", "#00FF00"))+
+  geom_point(alpha=0.6)+
+  xlab("Melanopic EDI") + 
+  ylab("Neutral Betas (a.u.)") + 
+  labs(tag = "L")+
+  labs(col = "Hypothalamus Subpart")+
+  theme_classic()+ 
+  theme(text = element_text(size = 16, face="bold"),
+        legend.text = element_text(size = 16, face="bold"), 
+        legend.title = element_text(size = 16),
+        legend.box = "horizontal")+
+  geom_linerange(aes(ymin=mean_beta-se,ymax=mean_beta+se))+
+  scale_x_continuous(breaks = c(0, 10, 37, 92, 190))
+
+
+### Combine plots 
+ggarrange(F2I, F2J, F2K, F2L, ncol = 2, nrow = 2)
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