R/SCRS_cdr.R

In gongyh/RamanD2O: RamanD2O: an R/Shiny app designed for the analysis of cellular Ramanome data

## calc C-D ratio of SCRS (after preprocess)

SCRS_cdr <- function(input_csv, output_dir) {
  dir.create(output_dir)

  SNR1 <- read.table(input_csv, header = TRUE, sep = ",")
  SNR2 <- SNR1[, 12:length(SNR1[1, ]) - 1]
  colnames(SNR2) <- formatC(
    as.numeric(gsub("spc.", "", colnames(SNR2))), digits = 1, format = "f"
  )
  wave_nums <- as.numeric(gsub("[A-Z]", "", colnames(SNR2)))
  CDR_All <- NULL
  for (i in seq_len(nrow(SNR2))) {
    CD_start <- which.min(abs(wave_nums - 2050))
    CD_end <- which.min(abs(wave_nums - 2300))
    CH_start <- which.min(abs(wave_nums - 3050))
    CH_end <- which.min(abs(wave_nums - 2800))
    CD <- SNR2[i, CD_start:CD_end]
    CH <- SNR2[i, CH_start:CH_end]
    CDR <- sum(CD) / (sum(CD) + sum(CH))
    CDR_All <- rbind(CDR_All, CDR)
  }
  CDR_All <- cbind(SNR1[, 1:7], data.frame(CDR = CDR_All))
  write.table(
    CDR_All,
    file = paste0(output_dir, "/", "CDR.txt"),
    sep = "\t",
    quote = FALSE,
    row.names = FALSE
  )

  pdf(
    paste0(output_dir, "/", "CDR.pdf"),
    width = 7,
    height = 5,
    useDingbats = FALSE
  )
  par(ps = 12)
  df <-
    read.table(paste0(output_dir, "/", "CDR.txt"),
      sep = "\t",
      header = TRUE
    )


  ggdotplot(
    df,
    x = "Group",
    y = "CDR",
    add = c("violin", "mean_sd"),
    size = 0.3
  ) +
    theme_bw() + xlab("Group") + ylab("CDR") + stat_compare_means() +
    theme(
      text = element_text(size = 12),
      panel.grid.major = element_blank(),
      panel.grid.minor = element_blank(),
      axis.text.x = element_text(color = "black"),
      axis.text.y = element_text(color = "black")
    )

  summary.stats <- df %>%
    select(c("Group", "CDR")) %>%
    group_by(Group) %>%
    get_summary_stats(type = "common")

  ggsummarytable(
    summary.stats,
    x = "Group",
    y = c("n", "min", "max", "mean", "median", "iqr", "sd", "se", "ci"),
    digits = 3,
    size = 6,
    ggtheme = theme_bw() +
      theme(
        text = element_text(size = 12),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(),
        axis.text.x = element_text(color = "black"),
        axis.text.y = element_text(color = "black")
      )
  )

  dev.off()
}