R/lodq_util.R

In Vitek-Lab/MSstatsLODQ: Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

#' @keywords internal
.bilinear <- function(x, intercept, slope, change) { 
  ifelse(x < change, intercept, slope * (x - change) + intercept) 
}

#' @keywords internal
.second <- function(x, intercept, slope, slope2) {
  slope2 * x * x + slope * x + intercept
}

#' @keywords internal
.bilinear_LOD <- function(x, intercept, slope, change) { 
  ifelse(x < change, intercept, slope * (x - change) + intercept) 
}

#' @keywords internal
.bilinear_LOD_nonlin <- function(x, intercept, slope, change,exponent) { 
  ifelse(x < change, intercept, slope * (x - change)^exponent + intercept) 
}

#' @keywords internal
.linear <- function(x, intercept, slope){
  slope * x + intercept
}

#' @keywords internal
.invlinear <- function(y, intercept, slope) {
  (y - intercept) / slope
}

#' @keywords internal
.fun_error <- function(dir, peptide, site, message) {
  filename <- paste(dir, "/", paste(peptide, "_", site, ".txt", sep = ""),
                   sep = "")
  write(message, file = filename)
}

#' @keywords internal
.ggplotColours <- function(n = 6, h = c(0, 360) + 15){
  if ((diff(h) %% 360) < 1) h[2] = h[2] - 360 / n
  hcl(h = (seq(h[1], h[2], length = n)), c = 100, l = 65)
}

#' @keywords internal
.theme_complete_bw <- function(base_size = 12, base_family = "") {
  theme_grey(base_size = base_size, base_family = base_family) +
    theme(
      axis.line = element_blank(),
      axis.text.x = element_text(size = base_size * 0.8 , lineheight = 0.9, 
                                 colour = "black", vjust = 1,
                                 margin = margin(5,0,10,0)),
      axis.text.y = element_text(size = base_size * 0.8, lineheight = 0.9, 
                                 colour = "black", hjust = 1, 
                                 margin = margin(0,5,0,10)),
      axis.ticks = element_line(colour = "black"),
      axis.title.x = element_text(size = base_size, vjust = 0.5),
      axis.title.y = element_text(size = base_size, angle = 90, vjust = 0.5),
      axis.ticks.length = unit(0.15, "cm"),
      
      legend.background = element_rect(colour=NA), 
      legend.key = element_rect(fill = NA, colour = "white", size = 0.25),
      legend.key.size = unit(1.2, "lines"),
      legend.text = element_text(size = base_size * 0.8),
      legend.title = element_text(size = base_size * 0.8, 
                                  face = "bold", hjust = 0),
      legend.position = "right",
      
      panel.background = element_rect(fill = "white", colour = NA), 
      panel.border = element_rect(fill = NA, colour = "black"), 
      panel.grid.major = element_line(colour = "gray75", size = 0.1,  
                                      linetype = 'dotted'), 
      panel.grid.minor = element_line(colour = "gray75", size = 0.25, 
                                      linetype = 'dotted'), 
      panel.margin = unit(0.25, "lines"),
      
      strip.background = element_rect(fill = NA, colour = NA), 
      strip.text.x = element_text(colour = "black", size = base_size * 0.8),
      strip.text.y = element_text(colour = "black", size = base_size * 0.8, angle = -90),
      
      plot.background =  element_rect(colour = NA, fill = "white"),
      plot.title = element_text(size = base_size * 1.2, margin = margin(0,0,10,0)),
      plot.margin = unit(c(1, 1, 0.5, 0.5), "lines"))
}