# efg, Stowers Institute for Medical Research
# July 2004.  Updated 8 Aug 2005.

#source("LombScargle.R")
source("http://research.stowers-institute.org/efg/2005/LombScargle/R/LombScargle.R")
unit <<- "hour"

# Assume calling program sets mfrow=c(2,2),if desired.
DemoLombScargleCosine <- function(period=48, N=48, Amplitude=1.0,
                                  LowFreq, HighFreq, MFactor=4,
                                  EvenSpacing=TRUE,
                                  FigureLabels="",
                                  Title="Cosine Curve (N=48)")
{
  if (EvenSpacing)
  {
    t <- 0:(N-1)     # hours
  } else {
    t <- sort( runif(N, 0, N) )
  }

  frequency <- 1/period
  ExpressionProfile <- Amplitude * cos(2*pi*frequency*t)

  M <- MFactor * N      # could be some other multiple of N
  TestFrequencies <- LowFreq + (HighFreq - LowFreq) * (1:M / M)
  Nindependent <- NHorneBaliunas(N)

  LS <- ComputeAndPlotLombScargle(t, ExpressionProfile, TestFrequencies,
                            Nindependent,
                            Title,
                            FigureLabels,
                            GridOption=FALSE,
                            IntervalHistogramOption=FALSE)

  return(LS)
}


DemoLombScargleCosineN <- function(period = 48, N=48, Amplitude=1.0,
                                   LowFreq=0.0, HighFreq=0.20, MFactor=4,
                                   FigureLabels="", Title="")
{
  # Compute Lomb-Scargle Periodogram

  if (Title == "")
  {
    Title <- paste("Cosine Curve (N=", N, ")", sep="")
  }

  t <- period * (1:N / N) # hours
  frequency <- 1/period
  ExpressionProfile <- Amplitude * cos(2*pi*frequency*t)

  M <- MFactor * N
  TestFrequencies <- LowFreq + (HighFreq - LowFreq) * (1:M / M)
  Nindependent <- NHorneBaliunas(N)

  LS <-  ComputeAndPlotLombScargle(t, ExpressionProfile, TestFrequencies,
                           Nindependent,
                           Title,
                           FigureLabels,
                           GridOption=FALSE,
                           IntervalHistogramOption=FALSE)
  return(LS)
}


DemoLombScargleCosineRandomN <- function(period = 48, N=48, Amplitude=1.0,
                                         LowFreq=0.0, HighFreq=0.20, MFactor=4,
                                         FigureLabels="")
{
  # Compute Lomb-Scargle Periodogram

  t <- period * (1:N / N) # hours

  t <- sort( runif(N, 0, period) )

  frequency <- 1/period
  ExpressionProfile <- Amplitude * cos(2*pi*frequency*t)

  M <- MFactor * N
  TestFrequencies <- LowFreq + (HighFreq - LowFreq) * (1:M / M)
  Nindependent <- NHorneBaliunas(N)

  LS <- ComputeAndPlotLombScargle(t, ExpressionProfile, TestFrequencies,
                          Nindependent,
                          paste("Cosine Curve (N=", N, ")", sep=""),
                          FigureLabels)
  return(LS)
}


DemoLombScargleCosineRandomNoise <- function(period = 48, N=48, Amplitude=1.0,
                                             LowFreq=0.0, HighFreq=0.20, MFactor=4,
                                             EvenSpacing=TRUE,
                                             Noise=1.0,
                                             FigureLabels="",
                                             Title="")
{
  if (Title == "")
  {
    Title <- paste("Cosine Curve + Noise (N=", N, ")", sep="")
  }

  if (EvenSpacing)
  {
    t <- 0:(N-1)
  } else {
    t <- sort( runif(N, 0, N) )
  }

  frequency <- 1/period
  ExpressionProfile <- Amplitude * cos(2*pi*frequency*t) + rnorm(N, mean=0, sd=Noise)

  M <- MFactor * N
  TestFrequencies <- LowFreq + (HighFreq - LowFreq) * (1:M / M)
  Nindependent <- NHorneBaliunas(N)

  LS <- ComputeAndPlotLombScargle(t, ExpressionProfile, TestFrequencies,
                          Nindependent,
                          Title,
                          FigureLabels,
                          GridOption=FALSE,
                          IntervalHistogramOption=FALSE)

  return(LS)
}


##########################################################################

DemoLombScargleNoise <- function(period=48, N=48,
                                 LowFreq=0.0, HighFreq=0.20, MFactor=4, Noise=1.0,
                                 EvenSpacing=FALSE,
                                 FigureLabels="", Title="")
{
  if (Title == "")
  {
    Title <- paste("Noise", sep="")
  }

  if (EvenSpacing)
  {
    t <- 0:(N-1)
  } else {
    t <- sort( runif(N, 0, N) )
  }

  frequency <- 1/period
  ExpressionProfile <- rnorm(N, mean=0, sd=Noise)

  M <- MFactor * N
  TestFrequencies <- LowFreq + (HighFreq - LowFreq) * (1:M / M)
  Nindependent <- NHorneBaliunas(N)

  LS <- ComputeAndPlotLombScargle(t, ExpressionProfile, TestFrequencies,
                          Nindependent,
                          Title,
                          FigureLabels,
                          GridOption=FALSE,
                          IntervalHistogramOption=FALSE)
  return(LS)
}


##########################################################################

DemoLombScargleCosine2 <- function(period1 = 24, period2 = 48, A1=1.0, A2=1.0,
                                   LowFreq, HighFreq, MFactor=4,
                                   EvenSpacing=TRUE,
                                   FigureLabels="", Noise=0.0, Title="")
{
  # Compute Lomb-Scargle Periodogram
  N <- 48

  if (Title == "")
  {
    Title <- "Sum of 2 Cosines (N=48)"
  }

  if (EvenSpacing)
  {
    t <- 0:(N-1)                    # hardwire over 48 hours for now
  } else {
    t <- sort( runif(N, 0, 48) )    # hardwire over 48 hours for now
  }

  frequency1 <- 1/period1
  frequency2 <- 1/period2

  ExpressionProfile <- A1*cos(2*pi*frequency1*t) + A2*cos(2*pi*frequency2*t) +
                       rnorm(N, mean=0, sd=Noise)

  M <- MFactor * N      # could be some other multiple of N
  TestFrequencies <- LowFreq + (HighFreq - LowFreq) * (1:M / M)
  Nindependent <- NHorneBaliunas(N)

  LS <- ComputeAndPlotLombScargle(t, ExpressionProfile, TestFrequencies,
                                  Nindependent,
                                  Title,
                                  FigureLabels="",
                                  GridOption=FALSE,
                                  IntervalHistogramOption=FALSE)
  return(LS)
}


DemoLombScargleCosine3 <- function(period1=24, period2=48, period3=60,
                                   A1=1.0, A2=1.0, A3=1.0,
                                   LowFreq, HighFreq, MFactor=4,
                                   EvenSpacing=TRUE,
                                   FigureLabels="",
                                   Noise=0.0,
                                   Title="")
{
  N <- 48                           # assume 48 hours

  if (Title == "")
  {
    Title <- "Sum of 3 Cosines (N=48)"
  }

  if (EvenSpacing)
  {
    t <- 0:(N-1)                    # hardwire over 48 hours for now
  } else {
    t <- sort( runif(N, 0, 48) )    # hardwire over 48 hours for now
  }

  frequency1 <- 1/period1
  frequency2 <- 1/period2
  frequency3 <- 1/period3

  ExpressionProfile <- A1*cos(2*pi*frequency1*t) + A2*cos(2*pi*frequency2*t) +
                       A3*cos(2*pi*frequency3*t) +
                       rnorm(N, mean=0, sd=Noise)

  M <- MFactor * N      # could be some other multiple of N
  TestFrequencies <- LowFreq + (HighFreq - LowFreq) * (1:M / M)
  Nindependent <- NHorneBaliunas(N)

  LS <- ComputeAndPlotLombScargle(t, ExpressionProfile, TestFrequencies,
                          Nindependent,
                          Title,
                          FigureLabels,
                          GridOption=FALSE,
                          IntervalHistogramOption=FALSE)
  return(LS)
}