CompExonSpace/CAGA_violin(Fig3F).Rmd at main · Novartis/CompExonSpace · GitHub

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```{r}
library(dplyr)
library(ggplot2)
library(ggpubr)
library(scales)
```


```{r}
# Define paths
data_dir <- Sys.getenv("MYDATA")

# function to load data
load_csv <- function(filename) {
  read.csv(file.path(data_dir, "exon_diff", filename), stringsAsFactors = FALSE)
}

# Load datasets
NVS <- load_csv("Exp1_NVSSM1_25nM_vs_DMSO.csv")

```


```{r}
NVS_AGA <- NVS %>%
  dplyr::filter(Exon3 == "AGA") %>%
  dplyr::filter(included == "yes") %>%
  dplyr::mutate(
    group = ifelse(Exon4 == "CAGA", "CAGA", "Other"))

my_comparisons <- list(c("Other", "CAGA"))

p <- ggplot(NVS_AGA,
            aes(x = group, y = HbondIntron, fill = group)) +

  # Violin
  geom_violin(trim = FALSE, alpha = 0.7, width = 1, color = "black") +

  # Dots on top
  geom_jitter(width = 0.12, size = 1.8, alpha = 0.8, color = "black") +

  scale_fill_manual(values = c("Other" = "grey70", "CAGA" = "grey40")) +

  labs(
    x = "",
    y = "Complementarity score",
    title = "Exp1 NVSSM1 25 nM: CAGA vs all other AGA exons"
  ) +

  theme_classic(base_size = 14) +
  theme(
    legend.position = "none",
    plot.title = element_text(hjust = 0.5, face = "bold"),
    axis.text = element_text(color = "black"),
    axis.line = element_line(color = "black"),
    axis.ticks = element_line(color = "black")
  )
p


```