# Load necessary libraries
library(ggplot2)
library(dplyr)

# Create dataset for mks-5
mks_5 <- data.frame(
  Minus_1 = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
  `0_second` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
  `50_second` = c(0.21, 0.31, 0.22, 0.15, 0.09, 0.20, 0.18, 0.12, 0.17, 0.10, 0.10, 0.10, 0.29, 0.34, 0.32, 0.19)
)

# Create dataset for bbs-7
bbs_7 <- data.frame(
  Minus_1 = c(1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00),
  `0_second` = c(0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00),
  `50_second` = c(0.05, 0.00, 0.04, 0.00, 0.02, 0.00, 0.00)
)

# Convert column names to valid variable names
names(mks_5) <- gsub("`", "_", names(mks_5))
names(bbs_7) <- gsub("`", "_", names(bbs_7))

# Function to calculate mean and SE
summary_stats <- function(df) {
  data.frame(
    Time = c(-1, 0, 50),
    Mean = c(mean(df$Minus_1), mean(df$X0_second, na.rm = TRUE), mean(df$X50_second, na.rm = TRUE)),
    SE = c(sd(df$Minus_1)/sqrt(length(df$Minus_1)), 
           sd(df$X0_second, na.rm = TRUE)/sqrt(length(df$X0_second)), 
           sd(df$X50_second, na.rm = TRUE)/sqrt(length(df$X50_second)))
  )
}

# Compute summary statistics for both datasets
plot_mks_5 <- summary_stats(mks_5) %>% mutate(Dataset = "mks-5")
plot_bbs_7 <- summary_stats(bbs_7) %>% mutate(Dataset = "bbs-7")

# Combine both datasets
combined <- rbind(plot_mks_5, plot_bbs_7)

# Define custom colors
my_colors <- c("red", "#006400")

# Create a new column for labels
combined$Label <- ifelse(combined$Dataset == "mks-5", "italic('mks-5')", "italic('bbs-7')")

# Plot with error bars
ggplot(combined, aes(x = Time, y = Mean, group = Dataset, color = Dataset)) +
  geom_smooth(method = "loess", se = FALSE, size = 1.3) +
  geom_point(size = 3) +
  geom_errorbar(aes(ymin = Mean - SE, ymax = Mean + SE), width = 2, size = 0.7) +
  scale_x_continuous(limits = c(-1, 50), name = "Time (s)") +
  scale_y_continuous(name = "Fluorescence Intensity") +
  theme(axis.line = element_line(color = "black", size = 1),
        axis.text = element_text(size = 16, color = "black", face = "bold"),
        axis.title = element_text(size = 16, color = "black", face = "bold"),
        panel.background = element_blank(),
        plot.background = element_blank(),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank()) +
  scale_color_manual(values = my_colors) +
  guides(color = FALSE) +
  geom_text(
    data = subset(combined, Time == 50),
    aes(label = Label, color = Dataset),
    size = 5,
    fontface = "bold",
    position = position_nudge(y = -0.05), # Adjust vertical position
    hjust = 0.5,
    parse = TRUE # Enables italic formatting
  )