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Visualization Source Code.Rmd
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Visualization Source Code.Rmd
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---
title: "R Code for Visualizations of EEG Data"
author: "Nicole Sullivan & Don Lyons"
date: "6/4/2017"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE)
```
```{r}
library(tidyverse)
erp_erd <- read_csv("ERP_ERD.csv")
```
## Stripcharts of Expressions in Angry and Neutral Tasks
```{r}
strip_theme <- theme(plot.title = element_text(family = "Times", face = "italic", hjust = 0.5, color = "gray45"),
plot.subtitle = element_text(family = "Times", face = "italic", hjust = 0.5, color = "gray45"),
axis.title = element_text(family = "Times", face = "italic", color = "gray45"),
axis.text = element_text(family = "Times", face = "italic", color = "gray45"),
strip.text.x = element_text(family = "Times", face = "italic", color = "gray45"),
strip.background = element_blank(),
legend.title = element_text(family = "Times", face = "italic", size = 8, color = "gray45"),
legend.text = element_text(family = "Times", color = "gray45", size = 8))
Cz_Fz_Pz <- erp_erd %>%
filter(Electrode == "Cz" | Electrode == "Pz" | Electrode == "Fz") %>%
mutate(LHA = ifelse(LHA == "NaN", 0, LHA)) %>%
mutate(LHA_levels = ifelse(LHA == 0, "0 - 5",
ifelse(LHA == 1, "0 - 5",
ifelse(LHA == 2, "0 - 5",
ifelse(LHA == 3, "0 - 5",
ifelse(LHA == 4, "0 - 5",
ifelse(LHA == 5, "0 - 5",
ifelse(LHA == 6, "6 - 10",
ifelse(LHA == 7, "6 - 10",
ifelse(LHA == 8, "6 -10",
ifelse(LHA == 9, "6 - 10",
ifelse(LHA == 10, "6 - 10",
ifelse(LHA == 11, "11 - 15",
ifelse(LHA == 12, "11 - 15",
ifelse(LHA == 13, "11 - 15",
ifelse (LHA == 14, "11 - 15",
ifelse(LHA == 15, "11 - 15",
ifelse(LHA == 16, "16 - 20",
ifelse(LHA == 17, "16 - 20",
ifelse(LHA == 18, "16 - 20",
ifelse(LHA == 19, "16 - 20",
ifelse(LHA == 20, "16 - 20", "21 - 25")))))))))))))))))))))) %>%
na.omit()
Cz_Fz_Pz %>%
filter(Task == "A") %>%
mutate(Expression = ifelse(Expression == "A", "Angry", "Happy")) %>%
ggplot(aes(Electrode, Mean_Amplitude)) +
geom_jitter(position=position_jitter(0.2), alpha = 0.7, aes(color = LHA_levels), size = 2) +
stat_summary(fun.y=median, geom="bar", fill ="darkgray", size = 1, alpha = 0.2) +
scale_color_manual(breaks = c("0 - 5", "6 - 10", "11 - 15", "16 - 20", "21 - 25"), values = c("0 - 5" = "#7fcdbb", "6 - 10" = "#41b6c4", "11 - 15" = "#1d91c0", "16 - 20" = "#225ea8", "21 - 25" = "#081d58")) +
labs(title = "T H E P 3 C O M P O N E N T",
subtitle = "following expressions in the angry task",
color = "LHA score",
y = "Mean Amplitude (in milliVolts)") +
facet_wrap(~Expression) +
strip_theme
```
```{r}
Cz_Fz_Pz %>%
filter(Task == "N") %>%
mutate(Expression = ifelse(Expression == "N", "Neutral", "Happy")) %>%
ggplot(aes(Electrode, Mean_Amplitude)) +
geom_jitter(position=position_jitter(0.2), alpha = 0.7, aes(color = LHA_levels), size = 2) +
stat_summary(fun.y=median, geom="bar", fill ="darkgray", size = 1, alpha = 0.2) +
scale_color_manual(breaks = c("0 - 5", "6 - 10", "11 - 15", "16 - 20", "21 - 25"), values = c("0 - 5" = "#7fcdbb", "6 - 10" = "#41b6c4", "11 - 15" = "#1d91c0", "16 - 20" = "#225ea8", "21 - 25" = "#081d58")) +
labs(title = "T H E P 3 C O M P O N E N T",
subtitle = "following expressions in the neutral task",
color = "LHA score",
y = "Mean Amplitude (in milliVolts)") +
facet_wrap(~Expression) +
strip_theme
```
## Race Boxplot for P3 in Angry Task
```{r}
Cz_Fz_Pz %>%
filter(Task == "N") %>%
mutate(Expression = ifelse(Expression == "N", "Neutral", "Happy")) %>%
mutate(Race = ifelse(Race == 1, "Caucasian",
ifelse(Race == 2, "African American",
ifelse(Race == 3, "Asian/Pacific Rim", "Hispanic")))) %>%
ggplot(aes(Electrode, Mean_Amplitude)) +
geom_boxplot(aes(color = Race, fill = Race), alpha = 0.5, width = 0.5) +
labs(title = "T H E P 3 C O M P O N E N T",
subtitle = "following expressions in the angry task",
y = "Amplitude (in milliVolts)") +
facet_wrap(~Expression) +
theme(plot.title = element_text(family = "Times", face = "italic", hjust = 0.5, color = "gray40"),
plot.subtitle = element_text(family = "Times", face = "italic", hjust = 0.5, color = "gray35"),
axis.title = element_text(family = "Times", face = "italic", color = "gray45"),
axis.text = element_text(family = "Times", face = "italic", color = "gray45"),
strip.text.x = element_text(family = "Times", face = "italic", color = "gray45"),
strip.background = element_blank(),
legend.position = "bottom",
legend.title = element_text(family = "Times", face = "italic", size = 8, color = "gray45"),
legend.text = element_text(family = "Times", color = "gray45", size = 8))
```
## Comparing Responses as a Function of Aggression
```{r}
erp_erd_data <- erp_erd %>%
mutate(Laterality = ifelse(Electrode == "C3" | Electrode == "P3" | Electrode == "F3", "L",
ifelse(Electrode == "Cz" | Electrode == "Pz" | Electrode == "Fz", "M",
ifelse(Electrode == "C4" | Electrode == "P4" | Electrode == "F4", "R", "NA")))) %>%
mutate(Anterior_Posterior = ifelse(Electrode == "F3" | Electrode == "Fz" | Electrode == "F4", "F",
ifelse(Electrode == "C3" | Electrode == "Cz" | Electrode == "C4", "C",
ifelse(Electrode == "P3" | Electrode == "Pz" | Electrode == "P4", "P", "NA")))) %>%
rename(Mean = Mean_Amplitude) %>%
gather(Mean, Delta, Theta, Alpha, Beta, Gamma, key = "Amplitude_Type", value = "Amplitude")
alpha_theta <- erp_erd_data %>%
filter(Electrode == "C3" | Electrode == "P3" | Electrode == "F3" | Electrode == "Cz" | Electrode == "Pz" | Electrode == "Fz" |
Electrode == "C4" | Electrode == "P4" | Electrode == "F4") %>%
filter(Amplitude_Type == "Alpha" | Amplitude_Type == "Theta")
alpha_theta %>%
filter(Task == "A") %>%
filter(Amplitude_Type == "Alpha") %>%
mutate(Expression = ifelse(Expression == "A", "Angry", "Happy")) %>%
mutate(Anterior_Posterior = ifelse(Anterior_Posterior == "C", "C3, Cz & C4",
ifelse(Anterior_Posterior == "F", "F3, Fz & F4", "P3, Pz & P4"))) %>%
na.omit %>%
ggplot(aes(LHA, Amplitude, color = Expression)) +
geom_point(alpha = 0.5) +
geom_smooth(se = FALSE) +
facet_wrap(~Anterior_Posterior) +
labs(title = "A N G R Y v. H A P P Y",
y = expression(paste(alpha, " amplitude (in mVs)"))) +
theme(plot.title = element_text(hjust = 0.5, size = 17, face = "italic",
family = "Times", color = "gray50"),
axis.title.x = element_text(hjust = 0.5, size = 9, face = "italic",
family = "Times", color = "gray50"),
axis.title.y = element_text(hjust = 0.5, size = 9, face = "italic",
family = "Times", color = "gray50"),
plot.caption = element_text(size = 8, color = "gray50", family = "Times"),
strip.text.x = element_text(family = "Times", face = "italic", color = "gray45"),
strip.background = element_blank(),
axis.text.x = element_text(family = "Times", color = "gray50"),
axis.text.y = element_text(family = "Times", color = "gray50"),
axis.ticks = element_line(color = "gray50"),
legend.position = "bottom",
legend.title = element_text(family = "Times", color = "gray50", size = 9),
legend.text = element_text(family = "Times", color = "gray50", size = 9, face = "italic"))
```
```{r}
alpha_theta %>%
filter(Task == "N" & Amplitude_Type == "Alpha") %>%
mutate(Expression = ifelse(Expression == "N", "Neutral", "Happy")) %>%
mutate(Anterior_Posterior = ifelse(Anterior_Posterior == "C", "C3, Cz & C4",
ifelse(Anterior_Posterior == "F", "F3, Fz & F4", "P3, Pz & P4"))) %>%
na.omit() %>%
ggplot(aes(LHA, Amplitude, color = Expression)) +
geom_point(alpha = 0.5) +
geom_smooth(se = FALSE) +
facet_wrap(~Anterior_Posterior) +
labs(title = "N E U T R A L v. H A P P Y",
y = expression(paste(alpha, " amplitude (in mVs)"))) +
theme(plot.title = element_text(hjust = 0.5, size = 17, face = "italic",
family = "Times", color = "gray50"),
axis.title.x = element_text(hjust = 0.5, size = 9, face = "italic",
family = "Times", color = "gray50"),
axis.title.y = element_text(hjust = 0.5, size = 9, face = "italic",
family = "Times", color = "gray50"),
plot.caption = element_text(size = 8, color = "gray50", family = "Times"),
panel.grid.minor = element_blank(),
strip.background = element_blank(),
strip.text = element_text(family = "Times", color = "gray50", face = "italic"),
axis.text.x = element_text(family = "Times", color = "gray50"),
axis.text.y = element_text(family = "Times", color = "gray50"),
axis.ticks = element_line(color = "gray50"),
legend.position = "bottom",
legend.title = element_text(family = "Times", color = "gray50", size = 9),
legend.text = element_text(family = "Times", color = "gray50", size = 9, face = "italic"))
```
# Comparing Group Responses Using Bar Charts
```{r}
library(plyr)
bar_chart_ang <- alpha_theta %>%
filter(Task == "A") %>%
filter(Amplitude_Type == "Alpha") %>%
mutate(Expression = ifelse(Expression == "A", "Angry", "Happy")) %>%
mutate(Anterior_Posterior = ifelse(Anterior_Posterior == "C", "C3, Cz & C4",
ifelse(Anterior_Posterior == "F", "F3, Fz & F4", "P3, Pz & P4"))) %>%
mutate(high_low_LHA = ifelse(LHA <= 12, "\u2264 12", "> 12")) %>%
filter(LHEA > 19) %>%
na.omit %>%
unite(Task_Exp_Axis_Group, Task, Expression, Anterior_Posterior, high_low_LHA)
avg_sd_ang <- plyr::ddply(bar_chart_ang, .(Task_Exp_Axis_Group), summarize, mean_amp = mean(Amplitude), sd_amp = sd(Amplitude))
bars_ang <- avg_sd_ang %>%
separate(Task_Exp_Axis_Group, into = c("Task", "Expression", "Anterior_Posterior", "high_low_LHA"), sep = "_") %>%
mutate(se_amp = sd_amp/sqrt(49)) %>%
mutate(ymax = mean_amp + se_amp,
ymin = mean_amp - se_amp)
ggplot(bars_ang, aes(high_low_LHA, mean_amp)) +
geom_bar(stat = "identity", fill = "lightsteelblue4", alpha = 0.6, width = 0.2) +
geom_errorbar(aes(ymin = mean_amp - se_amp, ymax = mean_amp + se_amp), width = 0.1, color = "gray40") +
facet_grid(Anterior_Posterior ~ Expression) +
scale_color_discrete(breaks = c("\u2264 12","> 12")) +
labs(subtitle = "for individuals with high experienced aggression, but differing committed aggression*",
title = "Alpha-Amplitude following Expressions in the Angry Task",
caption = "* for LHEA > 19 (median)",
x = "LHA Score",
y = expression(paste(alpha, " amplitude (in mVs)")),
color = "LHA") +
theme(plot.title = element_text(hjust = 0.5, size = 15, face = "italic",
family = "Times", color = "gray50"),
plot.subtitle = element_text(hjust = 0.5, size = 10, face = "italic",
family = "Times", color = "gray50"),
axis.title.x = element_text(hjust = 0.5, size = 9, face = "italic",
family = "Times", color = "gray50"),
axis.title.y = element_text(hjust = 0.5, size = 9, face = "italic",
family = "Times", color = "gray50"),
plot.caption = element_text(size = 8, color = "gray50", family = "Times"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(family = "Times", color = "gray50"),
axis.text.y = element_text(family = "Times", color = "gray50"),
axis.ticks = element_line(color = "gray50"),
legend.position = "bottom",
legend.title = element_text(family = "Times", color = "gray50", size = 9),
legend.text = element_text(family = "Times", color = "gray50", size = 9, face = "italic"),
strip.background = element_blank(),
strip.text = element_text(family = "Times", color = "gray50", face = "italic"))
```
```{r}
bar_chart_neu <- alpha_theta %>%
filter(Task == "N") %>%
filter(Amplitude_Type == "Alpha") %>%
mutate(Expression = ifelse(Expression == "N", "Neutral", "Happy")) %>%
mutate(Anterior_Posterior = ifelse(Anterior_Posterior == "C", "C3, Cz & C4",
ifelse(Anterior_Posterior == "F", "F3, Fz & F4", "P3, Pz & P4"))) %>%
mutate(high_low_LHA = ifelse(LHA <= 12, "\u2264 12", "> 12")) %>%
filter(LHEA > 19) %>%
na.omit %>%
unite(Task_Exp_Axis_Group, Task, Expression, Anterior_Posterior, high_low_LHA)
avg_sd_neu <- plyr::ddply(bar_chart_neu, .(Task_Exp_Axis_Group), summarize, mean_amp = mean(Amplitude), sd_amp = sd(Amplitude))
bars_neu <- avg_sd_neu %>%
separate(Task_Exp_Axis_Group, into = c("Task", "Expression", "Anterior_Posterior", "high_low_LHA"), sep = "_") %>%
mutate(se_amp = sd_amp/sqrt(49)) %>%
mutate(ymax = mean_amp + se_amp,
ymin = mean_amp - se_amp)
ggplot(bars_neu, aes(high_low_LHA, mean_amp)) +
geom_bar(stat = "identity", fill = "lightsteelblue4", alpha = 0.7, width = 0.2) +
facet_grid(Anterior_Posterior ~ Expression) +
scale_color_discrete(breaks = c("\u2264 12","> 12")) +
geom_errorbar(aes(ymin = mean_amp - se_amp, ymax = mean_amp + se_amp), width = 0.1, color = "gray40") +
labs(subtitle = "for individuals with high experienced aggression, but differing committed aggression*",
title = "Alpha-Amplitude following Expressions in the Neutral Task",
caption = "* for LHEA > 19 (median)",
x = "LHA score",
y = expression(paste(alpha, " amplitude (in mVs)")),
color = "LHA") +
theme(plot.title = element_text(hjust = 0.5, size = 15, face = "italic",
family = "Times", color = "gray50"),
plot.subtitle = element_text(hjust = 0.5, size = 10, face = "italic",
family = "Times", color = "gray50"),
axis.title.x = element_text(hjust = 0.5, size = 9, face = "italic",
family = "Times", color = "gray50"),
axis.title.y = element_text(hjust = 0.5, size = 9, face = "italic",
family = "Times", color = "gray50"),
plot.caption = element_text(size = 8, color = "gray50", family = "Times"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(family = "Times", color = "gray50"),
axis.text.y = element_text(family = "Times", color = "gray50"),
axis.ticks = element_line(color = "gray50"),
legend.position = "bottom",
legend.title = element_text(family = "Times", color = "gray50", size = 9),
legend.text = element_text(family = "Times", color = "gray50", size = 9, face = "italic"),
strip.background = element_blank(),
strip.text = element_text(family = "Times", color = "gray50", face = "italic"))
```