CompExonSpace/dPSI_pval(Fig1D_S1).Rmd at main · Novartis/CompExonSpace · GitHub

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```{r}
# Load libraries
library(ggplot2)
library(readr)
library(dplyr)

# Define paths
data_dir <- Sys.getenv("MYDATA")

```

```{r}

# function to load data (differential analysis provided)
load_exon_data <- function(filename) {
  read_csv(file.path(data_dir, "exon_diff", filename), show_col_types = FALSE)
}

# function to generate volcano plot (pval vs dPSI)
plot_volcano <- function(df, title) {
  ggplot(df, aes(x = altsplice_delta_psi,
                 y = -log10(altsplice_padj),
                 color = included)) +
    geom_point(alpha = 0.4) +
    labs(
      title = title,
      x = "dPSI",
      y = "-log10(p-value)"
    ) +
    ylim(0, 100) +
    theme_minimal() +
    theme(panel.grid = element_blank()) +
    coord_fixed(ratio = 0.04)
}

# datasets
SM1_25   <- load_exon_data("Exp1_NVSSM1_25nM_vs_DMSO.csv")
SM1_100  <- load_exon_data("Exp1_NVSSM1_100nM_vs_DMSO.csv")
Ris_655  <- load_exon_data("Exp1_Ris_655nM_vs_DMSO.csv")
Ris_1000 <- load_exon_data("Exp1_Ris_1uM_vs_DMSO.csv")
neg      <- load_exon_data("Exp1_neg.ctrl_vs_DMSO.csv")

NVS_mut  <- load_exon_data("Exp4_U1G6C7_NVSSM1_vs_U1G6C7.csv")
Ris_mut  <- load_exon_data("Exp4_U1G6C7_Ris_vs_U1G6C7.csv")

U1CU     <- load_exon_data("Exp3_U1CU_vs_U1wt.csv")


# Print plots
plot_volcano(SM1_25,   "Exp1 NVSSM1 25 nM vs DMSO")
plot_volcano(SM1_100,  "Exp1 NVSSM1 100 nM vs DMSO")
plot_volcano(Ris_655,  "Exp1 Ris 655 nM vs DMSO")
plot_volcano(Ris_1000, "Exp1 Ris 1 µM vs DMSO")
plot_volcano(neg,      "Exp1 Negative Control")

plot_volcano(NVS_mut,  "Exp4 NVSSM1 vs U1G6C7")
plot_volcano(Ris_mut,  "Exp4 Ris vs U1G6C7")

plot_volcano(U1CU,     "Exp3 U1CU vs U1wt")


```