library(readxl)
library(gplots)
library(tidyverse)

wild_type <- read_xlsx("/Users/oktayismailkaplan/Desktop/Manuscripts/BBSome/Figures/Data_analysis/ELMOD_TBG_Intensity.xlsx", 
                 sheet = 10)
colnames(wild_type)
View(wild_type)

wild_type <- setNames(wild_type, c("Length", "TBG-1", "ELMD-1"))
wild_type
#reshape data from wide to long format
wild_type_long <- wild_type %>% 
  pivot_longer(
    cols = -Length, 
    names_to = "Genotype", 
    values_to = "Fluorescence_intensity"
  )

#This allow users to change the orders of columns in desired directions
wild_type_long$Genotype <- factor(wild_type_long$Genotype, levels = c("ELMD-1", "TBG-1"))

wild_type_long

#Change size of X-axis and Y-axis text
#Use face = "bold"
ggplot(data = wild_type_long, 
       aes(x = Length, y = Fluorescence_intensity, color = Genotype, group = Genotype))+
  geom_line(size=1) + 
  labs(x = "Lenght (μm)", y = "Fluorescence Intensity", color = "Genotype") + 
  theme(plot.title = element_text(hjust = 1.0, size = 18, face = "bold"),
        axis.title = element_text(size = 18, face = "bold"),  
        axis.text = element_text(size = 15, face = "bold"),#Change font size
        legend.title = element_blank(), 
        legend.text = element_text(size = 14, face = "bold"))+ 
  scale_color_manual(values= c("ELMD-1" = "darkgreen", "TBG-1" = "darkred"))+
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
        panel.background = element_blank(), axis.line = element_line(colour = "black"))

#Remove the labels on the right side and place the labels on each line
ggplot(data = wild_type_long, 
       aes(x = Length, y = Fluorescence_intensity, color = Genotype, group = Genotype)) +
  geom_smooth(se = FALSE, size=1, method = "loess") +
  geom_text(data = subset(wild_type_long, Length == "2-3 μm"), 
            aes(label = Genotype, x = 2.5, y = Fluorescence_intensity), 
            hjust = 0, vjust = 1.5, size = 12, color = c("ELMD-1" = "darkred", "TBG-1" = "darkgreen"), fontface='bold') +
  labs(x = "Lenght (μm)", y = "Fluorescence Intensity", color = "Genotype") + 
  scale_color_manual(values= c("ELMD-1" = "darkgreen", "TBG-1" = "darkred"))+
  theme(plot.title = element_text(hjust = 1.0, size = 30, face = "bold"),
        axis.title = element_text(size = 30, face = "bold"),  
        axis.text = element_text(size = 30, face = "bold"),#Change font size
        axis.text.x = element_text(angle = 60, hjust = 1),
        legend.title = element_blank(), 
        legend.text = element_text(size = 30, face = "bold"))+ 
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
        panel.background = element_blank(), axis.line = element_line(colour = "black"),
        legend.position = "none")+
  guides(color = guide_legend(override.aes = list(size=4)))


#Save as a png Width: 1200, Height: 874







##############bbs-7#################

bbs_7 <- read_xlsx("/Users/oktayismailkaplan/Desktop/Manuscripts/BBSome/Figures/Data_analysis/ELMOD_TBG_Intensity.xlsx", 
                       sheet = 11)
colnames(bbs_7)
bbs_7 <- setNames(bbs_7, c("Length", "TBG-1", "ELMD-1"))

#reshape data from wide to long format
bbs_7_long <- bbs_7 %>% 
  pivot_longer(
    cols = -Length, 
    names_to = "Genotype", 
    values_to = "Fluorescence_intensity"
  )

#This allow users to change the orders of columns in desired directions
bbs_7_long$Genotype <- factor(bbs_7_long$Genotype, levels = c("ELMD-1", "TBG-1"))


ggplot(data = bbs_7_long, 
       aes(x = Length, y = Fluorescence_intensity, color = Genotype, group = Genotype)) +
  #geom_line(size=1)+ 
  geom_smooth(se = FALSE, size=1, method = "loess") +
  geom_text(data = subset(bbs_7_long, Length == "2-3 μm"), 
            aes(label = Genotype, x = 2.5, y = Fluorescence_intensity), 
            hjust = 0, vjust = 1.5, size = 12, color = c("ELMD-1" = "darkred", "TBG-1" = "darkgreen"), fontface='bold') +
  labs(x = "Lenght (μm)", y = "Fluorescence Intensity", color = "Genotype") + 
  scale_color_manual(values= c("ELMD-1" = "darkgreen", "TBG-1" = "darkred"))+
  theme(plot.title = element_text(hjust = 1.0, size = 30, face = "bold"),
        axis.title = element_text(size = 30, face = "bold"),  
        axis.text = element_text(size = 30, face = "bold"),#Change font size
        axis.text.x = element_text(angle = 60, hjust = 1),
        legend.title = element_blank(), 
        legend.text = element_text(size = 30, face = "bold"))+  
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
        panel.background = element_blank(), axis.line = element_line(colour = "black"),
        legend.position = "none")+
  guides(color = guide_legend(override.aes = list(size=4)))



##############mks-5#################

mks_5 <- read_xlsx("/Users/oktayismailkaplan/Desktop/Manuscripts/BBSome/Figures/Data_analysis/ELMOD_TBG_Intensity.xlsx", 
                   sheet = 13)
colnames(mks_5)


mks_5 <- setNames(mks_5, c("Length", "TBG-1", "ELMD-1"))

#reshape data from wide to long format
mks_5_long <- mks_5 %>% 
  pivot_longer(
    cols = -Length, 
    names_to = "Genotype", 
    values_to = "Fluorescence_intensity"
  )



#This allow users to change the orders of columns in desired directions
mks_5_long$Genotype <- factor(mks_5_long$Genotype, levels = c("ELMD-1", "TBG-1"))


ggplot(data = mks_5_long, 
       aes(x = Length, y = Fluorescence_intensity, color = Genotype, group = Genotype)) +
  #geom_line(size=1)+ 
  geom_smooth(se = FALSE, size=1, method = "loess") +
  geom_text(data = subset(mks_5_long, Length == "2-3 μm"), 
            aes(label = Genotype, x = 2.5, y = Fluorescence_intensity), 
            hjust = 0, vjust = 1.5, size = 12, color = c("ELMD-1" = "darkred", "TBG-1"= "darkgreen"), fontface='bold') +
  labs(x = "Lenght (μm)", y = "Fluorescence Intensity", color = "Genotype") + 
  scale_color_manual(values= c("ELMD-1" = "darkgreen", "TBG-1" = "darkred"))+
  theme(plot.title = element_text(hjust = 1.0, size = 30, face = "bold"),
        axis.title = element_text(size = 30, face = "bold"),  
        axis.text = element_text(size = 30, face = "bold"),#Change font size
        axis.text.x = element_text(angle = 60, hjust = 1),
        legend.title = element_blank(), 
        legend.text = element_text(size = 30, face = "bold"))+  
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
        panel.background = element_blank(), axis.line = element_line(colour = "black"),
        legend.position = "none")+
  guides(color = guide_legend(override.aes = list(size=4)))



bbs_8 <- read_xlsx("/Users/oktayismailkaplan/Desktop/Manuscripts/BBSome/Figures/Data_analysis/ELMOD_TBG_Intensity.xlsx", 
                   sheet = 12)

bbs_8 <- setNames(bbs_8, c("Length", "TBG-1", "ELMD-1"))

#reshape data from wide to long format
bbs_8_long <- bbs_8 %>% 
  pivot_longer(
    cols = -Length, 
    names_to = "Genotype", 
    values_to = "Fluorescence_intensity"
  )

#This allow users to change the orders of columns in desired directions
bbs_8_long$Genotype <- factor(bbs_8_long$Genotype, levels = c("TBG-1", "ELMD-1"))


ggplot(data = bbs_8_long, 
       aes(x = Length, y = Fluorescence_intensity, color = Genotype, group = Genotype)) +
  #geom_line(size=1)+ 
  geom_smooth(se = FALSE, size=1, method = "loess") +
  geom_text(data = subset(bbs_8_long, Length == "2-3 μm"), 
            aes(label = Genotype, x = 2.5, y = Fluorescence_intensity), 
            hjust = 0, vjust = 1.5, size = 12, color = c("ELMD-1" = "darkred", "TBG-1" = "darkgreen"), fontface='bold') +
  labs(x = "Lenght (μm)", y = "Fluorescence Intensity", color = "Genotype") + 
  scale_color_manual(values= c("ELMD-1" = "darkgreen", "TBG-1" = "darkred"))+
  theme(plot.title = element_text(hjust = 1.0, size = 30, face = "bold"),
        axis.title = element_text(size = 30, face = "bold"),  
        axis.text = element_text(size = 30, face = "bold"),#Change font size
        axis.text.x = element_text(angle = 60, hjust = 1),
        legend.title = element_blank(), 
        legend.text = element_text(size = 30, face = "bold"))+
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
        panel.background = element_blank(), axis.line = element_line(colour = "black"),
        legend.position = "none")+
  guides(color = guide_legend(override.aes = list(size=4)))