R/GeneDistribution_Violin_Plot.R

In qiuyugong-aifi/QCBATCH: This packages is used to perform QC of bacth effect

#' Title
#'
#' @param combined_dataset
#' @param plotly
#'
#' @return
#' @export
#'
#' @examples
GeneDistribution_Violin_Plot <- function(combined_dataset, plotly = "False") {
  if (typeof(combined_dataset) == "S4") {
    combined_dataframe <- combined_dataset[[]]
  } else {
    combined_dataframe <- combined_dataset
  }

  if (plotly == "False") {
    p <- ggplot(combined_dataframe, aes(
      x = batch_id, y = n_genes,
      color = batch_id
    )) +
      geom_violin(trim = FALSE) +
      geom_boxplot(width = 0.1)
  } else if (plotly == "True") {
    p <- combined_dataframe %>% plot_ly(
      x = ~batch_id,
      y = ~n_genes, split = ~batch_id, type = "violin",
      box = list(visible = T), meanline = list(visible = T)
    )
  }
  return(p)
}