shackett

library(dplyr)
library(tidyr)
library(impulse) # from github/shackett

timepts <- c(0, 5, 10, 20, 30, 40, 60, 90) # time points measured
measurement_sd <- 0.5 # standard deviation of Gaussian noise added to each observation
total_measurements <- 10000 # total number of genes
signal_frac <- 0.2 # what fraction of genes contain real signal

set.seed(1234)

shackett

parallel_fread <- function(path, mc.cores = parallel::detectCores(), header = TRUE, ...) {
  stopifnot(file.exists(path))
  
  dots <- list(...)
  fread_args <- dots[intersect(names(formals(fread)), names(dots))]
  
  if (any(c("skip", "nrows") %in% fread_args)) {
    stop(paste(intersect(c("skip", "nrows"), fread_args), collapse = " & "), " cannot be provided")
  }
    

shackett

extract_color_space <- function(hmin=0, hmax=360, cmin=0, cmax=180, lmin=0, lmax=100) {
  
  # This is a pared down version of the code to generate a 
  
  # Presently doesn't allow hmax > hmin (H is circular)
  # hmin: lower bound of hue (0-360)
  # hmax: upper bound of hue (0-360)
  # cmin: lower bound of chroma (0-180)
  # cmax: upper bound of chroma (0-180)
  # lmin: lower bound of luminance (0-100)

shackett

library(scales)
library(ggplot2)
library(gridExtra)
library(tidyr)

options(stringsAsFactors = F)

source_dist <- 0.5 # fraction of protonated source
uptake_rate <- 1000 # uptake of A
Vol = 1e7

shackett

shack_peakHeight <- function( inList ){
  
  #### For baseline subtraction and quantification using peak height ####
  # Save spectra baseline file in a list so that original and baseline 
  # subtracted spectra can be compared side-by-side
  # Quantification by the maximum value once the baseline has been removed
  
  require(baseline)
  
  if(!exists("outList")){