R/top_table.R

In leandroroser/RNASeqFunctions: Several functions for rna-seq analysis

#' Generate dynamic table
#' @param x data frame
#' @param top number of elements to show. Default all
#' @param filter_exp filter to apply of the style : column_name logical_condition value.
#' Example: "FDR < 0.1"
#' @param type analysis type. Differential expression (DE) or differential exon usage (DEU).
#' @export

top_table <- function(x, top = Inf, filter_exp = NULL, type = c("DE", "DEU")) {

  type <- match.arg(type)

  if(type == "DE") {
    x <- x$table
  }

  if(!is.null(filter_exp)) {
    x <- eval(parse(text = paste0("x[x$", filter_exp, ", ]")))
  }

   if(type == "DE") {
  x$up_down <- 1*(x$logFC > 0) + -1* (x$logFC < 0)
  x$logFC <- round(x$logFC, 2)
  x$logCPM <- round(x$logCPM, 2)
  x$LR <- round(x$LR, 2)
  x$PValue <- formatC(x$PValue, format = "e", digits = 2)
  x$FDR <- formatC(x$FDR, format = "e", digits = 2)
  } else {
    x$P.Value <- formatC(x$P.Value, format = "e", digits = 2)
    x$FDR <- formatC(x$FDR, format = "e", digits = 2)
  }


  if(!is.infinite(top)){
    x <- x[seq_len(top), ]
  }

  DT::datatable(x, filter = 'top', options = list(pageLength = 5, autoWidth = TRUE))
}