R/mIFTO.map.and.plot.decile.graphs.R

In AstroPathJHU/mIFTO: mIFTO: Multiplex Immunoflourescence Titration Optimization

######################### map.and.plot.decile.graphs ###########################

#'Used by PxP script to write out the decile type graphs
#'
#'Created By: Benjamin Green
#'Last Edited 07/30/2020
#'
#'Designed to write out the fraction of positivity data for the PxP script
#'
#'It is meant to be run through the PixelbyPixel function
#'
#' @param wd the main data root directory
#' @param Antibody_Opal the paired string for an antibody opal pair, designated
#' as "AB (Opal NNN)"
#' @param Antibody the string for an antibody
#' @param Slide_Desctipt a unique identifier for each slide to be analyzed
#' @param Concentration a numeric vector of concentrations used in the titration
#' @param Tables the table of statistics gathered by PxP
#' @param theme1 graphing theme
#' @param con_type the type of concentration vector to use factor or numeric
#' @param colors the color vectors for the t test and histograms
#' @param Antibody_Opal.snratio Antibody Opal string for sn ratio graphs
#' @param Antibody_Opal.ttest Antibody Opal string for ttest graphs
#' @param pb.Object progress bar object
#' @return exports the fraction spreadsheets
#' @export
#'
mIFTO.map.and.plot.decile.graphs <- function(
  wd, Antibody_Opal, Antibody, Slide_Descript, Concentration, Tables,
  theme1, con_type, colors, Antibody_Opal.snratio, Antibody_Opal.ttest,
  pb.Object){
  #
  mIFTO::mIFTO.doupdate.pgbar(96, pb.Object,
                        'Generating Decile Graphs')
  #
  sn.plots <- mIFTO::mIFTO.map.snratio.plots(
    wd, Antibody_Opal, Slide_Descript,
    Concentration, Tables$Tables.byimage,
    Antibody_Opal.snratio, theme1, con_type,
    'decile'
  )
  #
  tplots <- mIFTO::mIFTO.map.ttest.plots(
    wd, Antibody_Opal, Slide_Descript,
    Concentration, Tables$Tables.byimage,
    Antibody_Opal.ttest, theme1, colors, con_type,
    'decile'
  )
  #
  bx.plots <- mIFTO::mIFTO.map.boxplots.plots(
    wd, Antibody_Opal, Slide_Descript,
    Concentration, Tables$Tables.wholeslide,
    theme1, colors, con_type,
    'decile'
  )
  #
  # print some graphs
  #
  # pull names vectors together
  #
  lbl <- "Welch's t Test Graphs"
  lbl2 <- paste0(
    "Measures the difference between signal and noise accounting for ",
    "variation. Higher values indicate more separation.")
  #
  sn.plots.l <- (length(Slide_Descript) + 1)
  lbl <- c(lbl, rep("Mean S/N Ratio Graphs",
                    ceiling(sn.plots.l/ 4)))
  lbl <- c(lbl, rep("Median S/N Ratio Graphs",
                    ceiling(sn.plots.l/ 4)))
  lbl2 <- c(lbl2, rep(paste0(
    "Measures the difference between signal and noise using a simple ratio. ",
    "Higher values indicate more separation. Here the mean signal \nand noise ",
    "intensity values are used to compute a S/N ratio for each image. The ",
    "average and std-devs, across each set of images, are \nthen plotted below."),
    ceiling(sn.plots.l/ 4)))
  lbl2 <- c(lbl2, rep(paste0(
    "Measures the difference between signal and noise using a simple ratio.",
    " Higher values indicate more separation. Here the median signal \nand noise ",
    "intensity values are used to compute a S/N ratio for each image. The ",
    "average and std-devs, across each set of images, are \nthen plotted below."),
    ceiling(sn.plots.l/ 4)))
  #
  lbl <- c(lbl, bx.plots$lbl)
  lbl2 <- c(lbl2, bx.plots$lbl2)
  #
  plots <- c(tplots, sn.plots, bx.plots$bx.plots)
  #
  glist <- c(
    mIFTO::mIFTO.m.grid.arrange(
      plots, lbl, lbl2, 1, 1, (ceiling(length(plots))/4 + 1)
    )
  )
  gout <- gridExtra::marrangeGrob(grobs=glist,nrow=1,ncol=1,top=NULL)
  #
  str = paste0(wd,'/Results.pixels/',
               'Decile type Graphs for ', Antibody_Opal)
  #
  ggplot2::ggsave(paste0(str,'.pdf'),gout,
                  height = 9, width = 8.5, units = 'in', scale = 1, dpi = 300)
}