R/plot_filter.R

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

#' Plot count matrix to check filter cutoff
#'
#' Plot the total number of features removed from count matrix using different
#' low count cutoffs for both maximum and total reads
#'
#' @param x count matrix, data.frame or tibble
#' @param n maximum cutoff, default is to display 0 to 20
#'
#' @return A plot
#'
#' @author Chris Stubben
#'
#' @examples
#' \dontrun{
#'  plot_filter(counts)
#' }
#' @export

plot_filter <- function(x, n = 20){
   if(dplyr::is.tbl(x)) x <- as_matrix(x)
   n1 <- rowSums(x)
   n2 <- apply(x, 1, max, na.rm=TRUE)
   x1 <- table(factor( n1[n1 <= n], levels = 0:n))
   x2 <- table(factor( n2[n2 <= n], levels = 0:n))
   y <- cbind( x1, x2)
   z <- apply(y, 2, cumsum)
   graphics::matplot(rownames(z), z, pch=c(17, 19), col=c("red", "blue"),
      xlab="Count cutoff",  ylab="Total features removed")
   graphics::legend("bottomright", c("max", "total"), pch=c(19,17),
      col=c("blue", "red"), bty="n", inset=0.1, title="Filter")
}