R/plot_scatterreplicates.R

In demar01/RIC: RIC (RNA interaction capture)

#' Intensity patterns across replicate (proteins of interest get highlighted).
#'
#' \code{plot_scatterreplicates} generates a scatterplot for two rgiven inputs
#' (repx &repy) and highligths the intensities of viral proteins.
#'  
#' @param aggregated_peptides Dataframe
#' output from \code{\link{agregate_singlepeptides}}
#' @param protein_1 Character,
#' Name of selected protein (1) to highlight on the plot
#' @param protein_2 Character,
#' Name of selected protein (2) to highlight on the plot
#' @param xlimits Integer,
#' Sets the x-axis limits on plot.
#' @param ylimits Integer,
#' Sets the y-axis limits on plot.
#' @param col1 Character,
#' Sets the color to highlight protein_1 on the plot
#' @param col2 Character,
#' Sets the color to highlight protein_2 on the plot
#' @param repx Character,
#' Sets the replicate to represent on the x-axis
#' @param repy Character,
#' Sets the replicate to represent on the y-axis
#' @examples
#' if(interactive()){
#' plot_scatterreplicates(aggregatedWCL_batch,
# 'protein_1 = "SV_wt_nsP2", protein_2= "SV_wt_E2",
#' xlimits=c(20,34), ylimits=c(20,34),
#' repx = "hour18_1",repy = "hour18_2")
#' }
#' @return A scatter plot 
#' @import stringr
#' @export
plot_scatterreplicates <- function(aggregated_peptides,
                                   protein_1,
                                   protein_2,
                                   xlimits,
                                   ylimits,
                                   col1 = "red",
                                   col2 = "blue",
                                   repx = "hour18_1",
                                   repy = "hour18_2") {
  if (is.integer(xlimits)) {
    xlimits <- as.numeric(xlimits)
  }
  if (is.integer(ylimits)) {
    ylimits <- as.numeric(ylimits)
  }

  assertthat::assert_that(
    is.data.frame(aggregated_peptides),
    is.character(protein_1),
    is.character(protein_2),
    is.numeric(xlimits),
    length(xlimits) == 2,
    is.numeric(xlimits),
    length(xlimits) == 2,
    is.character(col1),
    length(col1) == 1,
    is.character(col2),
    length(col2) == 1,
    is.character(repx),
    length(repx) == 1,
    is.character(repy),
    length(repy) == 1
  )

  # show message in case this doesnt exists....
  grepl(protein_1, aggregated_peptides$ENSGid) -> A
  grepl(protein_2, aggregated_peptides$ENSGid) -> B

  # aggregated_peptides %>% ggplot()+geom_point(aes(Intensity.L.18_M_4,Intensity.L.4_18_M ))

  plot(
    aggregated_peptides[, str_which(repx, names(aggregated_peptides))],
    aggregated_peptides[, str_which(repy, names(aggregated_peptides))],
    col = alpha("gray", 0.2),
    pch = 19,
    xlim = xlimits,
    ylim = ylimits,
    xlab = str_glue("Abundance aggregated_peptides sample {repx}"),
    ylab = str_glue("Abundance aggregated_peptides sample {repy}")
  )
  title(main = str_glue("Protein Abundance in aggregated_peptides \n {repx} and {repy}"))

  points(aggregated_peptides[A, 4],
    aggregated_peptides[A, 7],
    col = col1,
    pch = 19
  )
  text(
    aggregated_peptides[A, 4],
    aggregated_peptides[A, 7],
    labels = str_remove(protein_1, "SV_wt_"),
    cex = 1,
    pos = 3
  )

  points(aggregated_peptides[B, 4],
    aggregated_peptides[B, 7],
    col = col2,
    pch = 19
  )
  text(
    aggregated_peptides[B, 4],
    aggregated_peptides[B, 7],
    labels = str_remove(protein_2, "SV_wt_"),
    cex = 1,
    pos = 3
  )
}