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3d_figures_correction.R
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<<<<<<< HEAD
# Define the corrected data without timepoint 1
if (!require(plotrix)) install.packages("plotrix")
library(plotrix)
library(tidyverse)
time_points <- c(0.11, 0.5, 1, 3, 10)
library(tidyverse)
time_points <- c(0.11,
0.5, 1, 3, 10)
# Integrate error values directly into the IVC data frame
IVC_data <- data.frame(
Time = factor(time_points, levels = time_points),
AGuIX_Signal = c(0.27,
0.65,
0.55,
0.40,
0.20
),
AGuIX_Error = c(0.16,
0.16,
0.20,
0.13,
0.12
),
Dotarem_Signal = c(-0.03,
0.35,
0.30,
0.19,
0.04
),
Dotarem_Error = c(0.22,
0.17,
0.16,
0.17,
0.12
),
Sig1 = c( 0.2802,
0.01074, 0.02637, 0.02916, 0.02726)
)
# Integrate error values directly into the Aorta data frame
Aorta_data <- data.frame(
Time = factor(time_points, levels = time_points),
AGuIX_Signal = c(
5.548945201,
0.619190801,
0.536298914,
0.353784247,
0.203349585
),
AGuIX_Error = c(
2.83,
0.17,
0.17,
0.11,
0.11
),
Dotarem_Signal = c(
5.29,
0.30,
0.33,
0.10,
-0.07
),
Dotarem_Error = c(
2.15,
0.23,
0.23,
0.18,
0.15
)
,
Sig2 = c( 0.9875,
0.007302, 0.0387, 0.02073, 0.06486)
)
# Define aesthetic elements for consistency
font_family <- "Helvetica"
font_size_title <- 45
font_size_axis_title <- 35
font_size_text <- 35
font_size_facet <- 45
# For IVC data
IVC_long <- IVC_data %>%
pivot_longer(
cols = c(AGuIX_Signal, AGuIX_Error, Dotarem_Signal, Dotarem_Error),
names_to = c("Agent", ".value"), # This determines how the names are assigned to new columns
names_pattern = "(.*)_(.*)"
)
# For Aorta data
Aorta_long <- Aorta_data %>%
pivot_longer(
cols = c(AGuIX_Signal, AGuIX_Error, Dotarem_Signal, Dotarem_Error),
names_to = c("Agent", ".value"), # Same as above for consistency
names_pattern = "(.*)_(.*)"
)
# Combine the IVC and Aorta datasets
combined_data <- bind_rows(
IVC_long %>% mutate(Location = "Inferior Vena Cava"),
Aorta_long %>% mutate(Location = "Abdominal Aorta")
)
# Plot
gg <- ggplot(combined_data, aes(x = Time, y = Signal, fill = Agent)) +
geom_bar(stat = "identity", position = position_dodge(width = 0.7), width = 0.6) +
geom_errorbar(aes(ymin = pmax(Signal - Error, 0.0), ymax = Signal + Error), width = 0.2, position = position_dodge(width = 0.7)) +
scale_fill_manual(values = c("AGuIX" = "lightblue", "Dotarem" = "gold")) +
facet_wrap(~Location, scales = "free_y") +
labs(x = "Time (min)", y = "[Gd] (mg/mL)") +
theme_minimal() +
theme(
text = element_text(family = font_family),
plot.title = element_text(size = font_size_title, face = "bold", hjust = 0.5),
axis.title = element_text(size = font_size_axis_title),
axis.title.y = element_text(size = font_size_axis_title, vjust = 1.0),
axis.text = element_text(size = font_size_text, face = "bold"),
axis.text.x = element_text(vjust = 0.15),
axis.text.y = element_text(hjust = 0.15),
legend.title = element_blank(),
legend.text = element_text(size = 35),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
strip.text = element_text(size = font_size_facet, face = "bold"),
axis.line = element_line(color = "black", size = 1)
) +
scale_y_continuous(expand = expansion(mult = c(0, 0.05)), limits = function(x) c(0, 11)) +
geom_vline(xintercept = c(2.5, 4.5), linetype = "dotted", color = "black") +
geom_text(data = filter(combined_data, Location == "Inferior Vena Cava"), aes(x = Inf, y = Inf, label = "Global p < 0.01**"), vjust = 1.45, hjust = 2.2, color = "red", size = 12) +
geom_text(data = filter(combined_data, Location == "Abdominal aorta"), aes(x = Inf, y = Inf, label = "Global p < 0.01**"), vjust = 1.45, hjust = 2.2, color = "red", size = 12) +
geom_hline(yintercept = 0.2, linetype = "dotted", color = "black", size = 1.5)
print(gg)
ggsave("output_plot.png", plot = gg, width = 9000, height = 2500, units = "px")
=======
# Define the corrected data without timepoint 1
if (!require(plotrix)) install.packages("plotrix")
library(plotrix)
library(tidyverse)
time_points <- c(0.11, 0.5, 1, 3, 10)
library(tidyverse)
time_points <- c(0.11,
0.5, 1, 3, 10)
# Integrate error values directly into the IVC data frame
IVC_data <- data.frame(
Time = factor(time_points, levels = time_points),
AGuIX_Signal = c(0.27,
0.65,
0.55,
0.40,
0.20
),
AGuIX_Error = c(0.16,
0.16,
0.20,
0.13,
0.12
),
Dotarem_Signal = c(-0.03,
0.35,
0.30,
0.19,
0.04
),
Dotarem_Error = c(0.22,
0.17,
0.16,
0.17,
0.12
),
Sig1 = c( 0.2802,
0.01074, 0.02637, 0.02916, 0.02726)
)
# Integrate error values directly into the Aorta data frame
Aorta_data <- data.frame(
Time = factor(time_points, levels = time_points),
AGuIX_Signal = c(
5.548945201,
0.619190801,
0.536298914,
0.353784247,
0.203349585
),
AGuIX_Error = c(
2.83,
0.17,
0.17,
0.11,
0.11
),
Dotarem_Signal = c(
5.29,
0.30,
0.33,
0.10,
-0.07
),
Dotarem_Error = c(
2.15,
0.23,
0.23,
0.18,
0.15
)
,
Sig2 = c( 0.9875,
0.007302, 0.0387, 0.02073, 0.06486)
)
# Define aesthetic elements for consistency
font_family <- "Helvetica"
font_size_title <- 45
font_size_axis_title <- 35
font_size_text <- 35
font_size_facet <- 45
# For IVC data
IVC_long <- IVC_data %>%
pivot_longer(
cols = c(AGuIX_Signal, AGuIX_Error, Dotarem_Signal, Dotarem_Error),
names_to = c("Agent", ".value"), # This determines how the names are assigned to new columns
names_pattern = "(.*)_(.*)"
)
# For Aorta data
Aorta_long <- Aorta_data %>%
pivot_longer(
cols = c(AGuIX_Signal, AGuIX_Error, Dotarem_Signal, Dotarem_Error),
names_to = c("Agent", ".value"), # Same as above for consistency
names_pattern = "(.*)_(.*)"
)
# Combine the IVC and Aorta datasets
combined_data <- bind_rows(
IVC_long %>% mutate(Location = "Inferior Vena Cava"),
Aorta_long %>% mutate(Location = "Abdominal Aorta")
)
# Plot
gg <- ggplot(combined_data, aes(x = Time, y = Signal, fill = Agent)) +
geom_bar(stat = "identity", position = position_dodge(width = 0.7), width = 0.6) +
geom_errorbar(aes(ymin = pmax(Signal - Error, 0.0), ymax = Signal + Error), width = 0.2, position = position_dodge(width = 0.7)) +
scale_fill_manual(values = c("AGuIX" = "lightblue", "Dotarem" = "gold")) +
facet_wrap(~Location, scales = "free_y") +
labs(x = "Time (min)", y = "[Gd] (mg/mL)") +
theme_minimal() +
theme(
text = element_text(family = font_family),
plot.title = element_text(size = font_size_title, face = "bold", hjust = 0.5),
axis.title = element_text(size = font_size_axis_title),
axis.title.y = element_text(size = font_size_axis_title, vjust = 1.0),
axis.text = element_text(size = font_size_text, face = "bold"),
axis.text.x = element_text(vjust = 0.15),
axis.text.y = element_text(hjust = 0.15),
legend.title = element_blank(),
legend.text = element_text(size = 35),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
strip.text = element_text(size = font_size_facet, face = "bold"),
axis.line = element_line(color = "black", size = 1)
) +
scale_y_continuous(expand = expansion(mult = c(0, 0.05)), limits = function(x) c(0, 11)) +
geom_vline(xintercept = c(2.5, 4.5), linetype = "dotted", color = "black") +
geom_text(data = filter(combined_data, Location == "Inferior Vena Cava"), aes(x = Inf, y = Inf, label = "Global p < 0.01**"), vjust = 1.45, hjust = 2.2, color = "red", size = 12) +
geom_text(data = filter(combined_data, Location == "Abdominal aorta"), aes(x = Inf, y = Inf, label = "Global p < 0.01**"), vjust = 1.45, hjust = 2.2, color = "red", size = 12) +
geom_hline(yintercept = 0.2, linetype = "dotted", color = "black", size = 1.5)
print(gg)
ggsave("output_plot.png", plot = gg, width = 9000, height = 2500, units = "px")
>>>>>>> 77a3982bf0902d3f28a8584daad61788e60cc341