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07-02-2024_cass_BHRC_QuintileADHDInvestigation.R
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source("functions_to_source.R")
# Phenotype ADHD
pADHD <-
pheno %>%
select(IID, wave, dcanyhk) %>%
pivot_wider(
names_from = wave,
values_from = dcanyhk)
# Values ADHD
vADHD <-
prs %>%
select(IID, ADHD) %>%
rename(PRS = ADHD)
# Covariables for regression correction
cADHD <-
plyr::join_all(
list(sex, ages, state, pc),
by = "IID",
type = "inner"
)
# data from ADHD
dADHD <-
plyr::join_all(
list(pADHD, vADHD, cADHD),
by = "IID",
type = "inner"
)
# Quintiles
for_plot <-
dADHD %>%
mutate(
Deciles = ntile(PRS, 10),
Deciles = case_when(
Deciles == 1 ~ "1st",
Deciles == 2 ~ "2nd",
Deciles == 3 ~ "3rd",
Deciles == 4 ~ "4th",
Deciles == 5 ~ "5th",
Deciles == 6 ~ "6rd",
Deciles == 7 ~ "7th",
Deciles == 8 ~ "8th",
Deciles == 9 ~ "9th",
Deciles == 10 ~ "10th"
),
Quintiles = ntile(PRS, 5),
Quintiles = case_when(
Quintiles == 1 ~ "1st",
Quintiles == 2 ~ "2nd",
Quintiles == 3 ~ "3rd",
Quintiles == 4 ~ "4th",
Quintiles == 5 ~ "5th"
),
Conversion = case_when(
W0 == 0 & W1 == 0 & W2 == 0 ~ "control",
W0 == 0 & W1 == 0 & W2 == 2 ~ "in W2",
W0 == 0 & W1 == 2 ~ "in W1",
W0 == 2 ~ "in W0")) %>%
select(sex, popID, Conversion, Deciles, Quintiles, PC1, PC2)
# PCA Quintile
ggplot(for_plot,
aes(PC1, PC2,
color = Quintiles,
shape = sex,
fill = Quintiles,
label = Conversion)) +
geom_point(size = 6, alpha = 0.5) +
labs(
title = glue("BHRC ADHD PCA data by quintile and sex (N = {nrow(for_plot)})"),
subtitle = "PRS adjusted to sex, state, age (in all waves), and 20 first PCs",
caption = "04-03-2024_cass_BHRC_QuintileADHDInvestigation.R"
) +
scale_shape_manual(values = c("Female" = 24, "Male" = 22)) +
scale_fill_manual(values = c("1st" = "#6dc26d", "2nd" = "#009dff", "3rd" = "#b44545", "4th" = "orange", "5th" = "#7d45a0")) +
scale_color_manual(values = c("1st" = "#6dc26d", "2nd" = "#009dff", "3rd" = "#b44545", "4th" = "orange", "5th" = "#7d45a0")) +
theme_publish() +
theme(
text = element_text(family = font),
axis.text = element_text(size = 15),
axis.title = element_text(size = 20),
legend.title = element_text(size = 20),
legend.text = element_text(size = 20),
plot.caption = element_text(size = 20),
plot.subtitle = element_text(size = 20),
plot.title = element_text(size = 30)
)
# PCA Decile
ggplot(for_plot,
aes(PC1, PC2,
color = Deciles,
shape = sex,
fill = Deciles,
label = Conversion)) +
geom_point(size = 6, alpha = 0.5) +
labs(
title = glue("BHRC ADHD PCA data by decile and sex (N = {nrow(for_plot)})"),
subtitle = "PRS adjusted to sex, state, age (in all waves), and 20 first PCs",
caption = "04-03-2024_cass_BHRC_QuintileADHDInvestigation.R"
) +
scale_shape_manual(values = c("Female" = 24, "Male" = 22)) +
scale_color_manual(
values = c(
"1st" = "#387cb4", "2nd" = "#ff9100",
"3th" = "#db74df", "4th" = "#ace676",
"5th" = "#56ccc6", "6th" = "#d86f6f",
"7th" = "#51a589", "8th" = "#7051b8",
"9th" = "#c8df74", "10th" = "#dfbd74")) +
scale_fill_manual(values = c(
"1st" = "#387cb4", "2nd" = "#ff9100",
"3th" = "#db74df", "4th" = "#ace676",
"5th" = "#56ccc6", "6th" = "#d86f6f",
"7th" = "#51a589", "8th" = "#7051b8",
"9th" = "#c8df74", "10th" = "#dfbd74")) +
theme_publish() +
theme(
text = element_text(family = font),
axis.text = element_text(size = 15),
axis.title = element_text(size = 20),
legend.title = element_text(size = 20),
legend.text = element_text(size = 20),
plot.caption = element_text(size = 20),
plot.subtitle = element_text(size = 20),
plot.title = element_text(size = 30))
# Quintiles composition
ggthemr("fresh")
# Conversion time
p1 <- for_plot %>%
group_by(Conversion, Quintiles) %>%
summarise(N = n()) %>%
group_by(Quintiles) %>%
mutate(Proportion = N / sum(N)) %>%
ggplot(aes(Quintiles, Proportion, fill = Conversion)) +
geom_bar(
position = "fill",
stat = "identity",
alpha = 0.95,
width = 0.7) +
geom_text(aes(
label = N, y = Proportion),
position = position_fill(vjust = 0.5),
size = 7,
fontface = "italic") +
theme_minimal() +
labs(
title = glue("BHRC ADHD Quintiles composition (N = {nrow(for_plot)})"),
subtitle = "PRS adjusted to sex, state, age (in all waves), and 20 first PCs") +
theme(
text = element_text(family = font, color = "black"),
axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.line.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.line.y = element_blank(),
legend.position = "top",
legend.text = element_text(size = 20),
legend.title = element_blank(),
plot.title = element_text(size = 30, face = "bold"),
plot.subtitle = element_text(size = 20),
plot.caption = element_text(size = 20, hjust = 0.5, vjust = 2))
# Sex
p2 <- for_plot %>%
group_by(sex, Quintiles) %>%
summarise(N = n()) %>%
group_by(Quintiles) %>%
mutate(Proportion = N / sum(N)) %>%
ggplot(aes(Quintiles, Proportion, fill = sex)) +
geom_bar(
position = "fill",
stat = "identity",
alpha = 0.95,
width = 0.7) +
geom_text(aes(
label = N, y = Proportion),
position = position_fill(vjust = 0.5),
size = 7,
fontface = "italic") +
theme_minimal() +
theme(
text = element_text(family = font, color = "black"),
axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.line.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.line.y = element_blank(),
legend.position = "top",
legend.text = element_text(size = 20),
legend.title = element_blank(),
plot.title = element_text(size = 35, face = "bold"),
plot.subtitle = element_text(size = 30),
plot.caption = element_text(size = 20, hjust = 0.5, vjust = 2))
# State
p3 <- for_plot %>%
group_by(popID, Quintiles) %>%
summarise(N = n()) %>%
group_by(Quintiles) %>%
mutate(Proportion = N / sum(N)) %>%
ggplot(aes(Quintiles, Proportion, fill = popID)) +
geom_bar(
position = "fill",
stat = "identity",
alpha = 0.95,
width = 0.7) +
geom_text(aes(
label = N, y = Proportion),
position = position_fill(vjust = 0.5),
size = 7,
fontface = "italic") +
scale_fill_manual(values = c("BRA_SP" = "#699b7f", "BRA_RS" = "#994e6d")) +
labs(caption = "04-03-2024_cass_BHRC_QuintileADHDInvestigation.R") +
theme_minimal() +
theme(
text = element_text(family = font, color = "black"),
axis.title.x = element_text(size = 25, face = "bold", color = "black"),
axis.text.x = element_text(size = 25, face = "bold", color = "black"),
axis.line.x = element_line(linewidth = 1),
axis.ticks.x = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.line.y = element_blank(),
legend.position = "top",
legend.text = element_text(size = 20),
legend.title = element_blank(),
plot.title = element_text(size = 35, face = "bold"),
plot.subtitle = element_text(size = 30),
plot.caption = element_text(size = 20, hjust = 0.5, vjust = 1))
library(patchwork)
p1 / p2 / p3