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INT_by_task.Rmd
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---
title: "INT_by_task"
author: "Shane Devine McKeon"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(LNCDR)
library(dplyr)
library(ggplot2)
library(mgcv)
library(lme4)
library(lmerTest)
library(tidyr)
library(gratia)
library(tidyverse)
library(ggeffects)
library(marginaleffects)
library(extrafont)
extrafont::loadfonts()
library(conflicted)
library(eegkit)
conflict_prefer("filter", "dplyr") # Always use dplyr::filter()
```
# Whole Brain
```{r}
avgACW_allDelaysavg <- read.csv('/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Entropy/Results/acw/MGS/twoSecondSegments/allSubjects_AvgDelayEpochs_wholeBrain.csv')
avgACW_allDelaysavg$epoch <- 'Delay'
avgACW_rest <- read.csv('/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Entropy/Results/acw/Rest/twoSecondSegments/allSubjects_avgTrialsChansEpochs_rest.csv')
names(avgACW_rest)[names(avgACW_rest) == "urchan"] <- "channel"
avgACW_rest <- avgACW_rest %>% filter(epoch == 'restEyesOpen') %>% select("lunaid", "age", "sex", "visitno", "ACW_50", "ageGroup")
avgACW_rest$epoch <- 'Rest'
delay_rest <- rbind(avgACW_allDelaysavg, avgACW_rest)
delay_rest$epoch <- as.factor(delay_rest$epoch)
```
```{r}
lunaize(
ggplot(data = delay_rest,
aes(x = factor(epoch, levels = c("Rest", "Delay")), y = ACW_50, fill = epoch)) +
geom_boxplot(alpha = 0.8, position = position_dodge(width = 0.75), color = "black", width=0.35) +
geom_line(aes(group= interaction(lunaid)), alpha = 0.2, linewidth=0.1) +
labs(x = "Seconds Epoch", y = "ACW", fill = "Task") +
theme_minimal()
) + scale_fill_manual(values = c("#012b0d", "#27763d")) +
theme(
legend.position = "right",
axis.text = element_text(size = 20, color = c("black")),
axis.title.x = element_text(size = 20, color = c("black")),
axis.title.y = element_text(size = 20, color = c("black")),
axis.line = element_line(linewidth = .2),
axis.ticks = element_line(linewidth = .2))
delay_rest_wide <- delay_rest %>%
pivot_wider(names_from = epoch, # Column to use for creating new column names
values_from = ACW_50) # Column to use for filling the values in new columns
t.test(delay_rest_wide$Delay, delay_rest_wide$Rest, paired = TRUE)
ggsave(filename = "/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Entropy/Results/Figures/Figure2/INT_task_boxplot_wholeBrain.pdf", device = "pdf", dpi = 500, width = 8, height = 6)
```
# Regions
## EEG Fig
```{r}
chanLocs <- read.csv('/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Entropy/Results/ChannelLocs.csv')
F_labels <- chanLocs$labels[grep("^F", chanLocs$labels)]
A_labels <- chanLocs$labels[grep("^A", chanLocs$labels)]
P_labels <- chanLocs$labels[grep("^P", chanLocs$labels)]
O_labels <- chanLocs$labels[grep("^O", chanLocs$labels)]
pdf("/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Entropy/Results/Figures/Figure2/frontalEEGplot.pdf", width = 5, height = 5)
eegkit::eegcap(electrodes = c("Fp1", "F7", "F5", "F3", "F1", "FC1", "FC3", "FC5", "FT9", "Fp2", "F8", "F6", "F4", "F2", "Fz", "FCz", "FC2", "FC4", "FC6", "FT10", #Frontal
"AF1", "AF5", "AFz", "AF2", "AF6","Cz", "C1", "C2"),
col.point = c("#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d", "#012b0d","#012b0d","#012b0d"),
cex.point = 3, nose = TRUE, ears = TRUE,
plotlabels = FALSE, plotaxes = FALSE, col.head = "grey", type="2d")
dev.off()
```
```{r}
pdf("/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Entropy/Results/Figures/Figure2/parietalEEGplot.pdf", width = 5, height = 5)
eegkit::eegcap(electrodes = c("P9", "P7", "P5", "P3", "P1", "PO3", "PO7", "PO9", "POz", "Pz", "P10", "P8", "P6", "P4", "P2", "PO4", "PO8", "PO10"), #Parietal
col.point = c( "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d", "#27763d"),
cex.point = 3, nose = TRUE, ears = TRUE,
plotlabels = FALSE, plotaxes = FALSE, col.head = "grey", type="2d")
dev.off()
```
```{r}
pdf("/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Entropy/Results/Figures/Figure2/OccipitalEEGplot.pdf", width = 5, height = 5)
eegkit::eegcap(electrodes = c("O1", "Oz", "O2","I1", "I2"), #Occipital
col.point = c("#90b8a6", "#90b8a6", "#90b8a6", "#90b8a6", "#90b8a6"),
cex.point = 3, nose = TRUE, ears = TRUE,
plotlabels = FALSE, plotaxes = FALSE, col.head = "grey", type="2d")
dev.off()
```
## All Subjects
```{r}
avgACW_allEpochs <- read.csv('/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Entropy/Results/acw/MGS/twoSecondSegments/allSubjects_allEpochs_regions.csv') %>% filter(epoch == 'Delays' | epoch == 'restEyesOpen') %>%
select(-ACW_0)
lunaize(
ggplot(data = avgACW_allEpochs,
aes(x = factor(epoch, levels = c("restEyesOpen", "Delays")), y = ACW_50, fill = interaction(epoch))) +
geom_boxplot(alpha = 0.8, position = position_dodge(width = 0.75), color = "black", width=0.35) +
geom_line(aes(group= interaction(lunaid)), alpha = 0.2, linewidth=0.1) +
labs(x = "Epoch", y = "ACW", fill = "Task") +
theme_minimal()
) + scale_fill_manual(values = c("#012b0d", "#27763d")) +
theme(
legend.position = "none",
axis.text = element_text(size = 20, color = c("black")),
axis.title.x = element_text(size = 20, color = c("black")),
axis.title.y = element_text(size = 20, color = c("black")),
axis.line = element_line(linewidth = .2),
axis.ticks = element_line(linewidth = .2),
strip.background = element_rect(fill = "white")) + facet_wrap(~region)
wide <- avgACW_allEpochs %>%
unite("epoch_region", epoch, region, sep = "_") %>%
pivot_wider(names_from = "epoch_region", values_from = ACW_50)
t.test(wide$Delays_Frontal, wide$restEyesOpen_Frontal, paired = TRUE)
t.test(wide$Delays_Occipital, wide$restEyesOpen_Occipital, paired = TRUE)
t.test(wide$Delays_Parietal, wide$restEyesOpen_Parietal, paired = TRUE)
ggsave(filename = "/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Entropy/Results/Figures/Figure2/INT_task_boxplot_regions.pdf", device = "pdf", dpi = 500, width = 18, height = 6)
```
## Adults Only
```{r}
lunaize(
ggplot(data = avgACW_allEpochs %>% filter(ageGroup == 'Adults'),
aes(x = epoch, y = ACW_50, fill = interaction(epoch))) +
geom_boxplot(alpha = 0.8, position = position_dodge(width = 0.75), color = "black", width=0.35) +
geom_line(aes(group= interaction(lunaid)), alpha = 0.2, linewidth=0.1) +
labs(x = "Epoch", y = "ACW", fill = "Task", title = 'Over 18') +
theme_minimal()
) + scale_fill_manual(values = c("#012b0d", "#27763d")) +
theme(
legend.position = "right",
axis.text = element_text(size = 20, color = c("black")),
axis.title.x = element_text(size = 20, color = c("black")),
axis.title.y = element_text(size = 20, color = c("black")),
axis.line = element_line(linewidth = .2),
axis.ticks = element_line(linewidth = .2)) + facet_wrap(~region)
wide <- avgACW_allEpochs %>% filter(ageGroup == 'Adults') %>%
unite("epoch_region", epoch, region, sep = "_") %>%
pivot_wider(names_from = "epoch_region", values_from = ACW_50)
t.test(wide$Delays_Frontal, wide$restEyesOpen_Frontal, paired = TRUE)
t.test(wide$Delays_Occipital, wide$restEyesOpen_Occipital, paired = TRUE)
t.test(wide$Delays_Parietal, wide$restEyesOpen_Parietal, paired = TRUE)
ggsave(filename = "/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Entropy/Results/Figures/Figure2/INT_task_boxplot_regions_adults.pdf", device = "pdf", dpi = 500, width = 15, height = 6)
```
## Adolescence Only
```{r}
lunaize(
ggplot(data = avgACW_allEpochs %>% filter(ageGroup == 'Adol'),
aes(x = epoch, y = ACW_50, fill = interaction(epoch))) +
geom_boxplot(alpha = 0.8, position = position_dodge(width = 0.75), color = "black", width=0.35) +
geom_line(aes(group= interaction(lunaid)), alpha = 0.2, linewidth=0.1) +
labs(x = "Epoch", y = "ACW", fill = "Task", title = 'Under 18') +
theme_minimal()
) + scale_fill_manual(values = c("#012b0d", "#27763d")) +
theme(
legend.position = "right",
axis.text = element_text(size = 20, color = c("black")),
axis.title.x = element_text(size = 20, color = c("black")),
axis.title.y = element_text(size = 20, color = c("black")),
axis.line = element_line(linewidth = .2),
axis.ticks = element_line(linewidth = .2)) + facet_wrap(~region)
wide <- avgACW_allEpochs %>% filter(ageGroup == 'Adol') %>%
unite("epoch_region", epoch, region, sep = "_") %>%
pivot_wider(names_from = "epoch_region", values_from = ACW_50)
t.test(wide$Delays_Frontal, wide$restEyesOpen_Frontal, paired = TRUE)
t.test(wide$Delays_Occipital, wide$restEyesOpen_Occipital, paired = TRUE)
t.test(wide$Delays_Parietal, wide$restEyesOpen_Parietal, paired = TRUE)
ggsave(filename = "/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Entropy/Results/Figures/Figure2/INT_task_boxplot_regions_adol.pdf", device = "pdf", dpi = 500, width = 15, height = 6)
```
## Both adults and adolescence on one plot
```{r}
lunaize(ggplot(data = avgACW_allEpochs, aes(x = ageGroup, y = ACW_50, fill = interaction(factor(epoch, levels = c("restEyesOpen", "Delays"))))) +
geom_boxplot(alpha = 0.8, position = position_dodge(width = 0.75), color = "black", width = 0.35) +
labs(x = "Epoch", y = "ACW", fill = "Task") +
theme_minimal() +
scale_fill_manual(values = c("#012b0d", "#27763d", "#012b0d", "#27763d", "#012b0d", "#27763d"))) +
theme(
legend.position = 'right',
axis.text = element_text(size = 20, color = "black"), # Removed vectorized input here
axis.title.x = element_text(size = 20, color = "black"), # Removed vectorized input here
axis.title.y = element_text(size = 20, color = "black"), # Removed vectorized input here
axis.line = element_line(linewidth = 0.2),
axis.ticks = element_line(linewidth = 0.2),
strip.background = element_rect('white')) +
facet_wrap(~factor(region, levels = c("Frontal", "Parietal", "Occipital")))
wide <- avgACW_allEpochs %>%
unite("epoch_region", epoch, region, sep = "_") %>%
pivot_wider(names_from = "epoch_region", values_from = ACW_50)
t.test(wide$Delays_Frontal, wide$restEyesOpen_Frontal, paired = TRUE)
t.test(wide$Delays_Occipital, wide$restEyesOpen_Occipital, paired = TRUE)
t.test(wide$Delays_Parietal, wide$restEyesOpen_Parietal, paired = TRUE)
ggsave(filename = "/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Entropy/Results/Figures/Figure3/INT_task_boxplot_regions_adolAdults.pdf", device = "pdf", dpi = 500, width = 18, height = 6)
```