fnc.R

#' simple find the peaks in an univariate serie
#' replace all non peaks by 0
#'
#' @param threshold
#' @param nsamples.ignore number of sample after a peaks to ignore (avoid false detection)
#' @param norm TRUE to normalize peaks to 1, FALSE keep the value of the peaks


findPeaks <- function(x, threshold=50, nsamples.ignore=1000, norm=FALSE){
  N  <- length(x)
  it <- 1
  
  
  # Clearly not an R friendly piece of code, but didn't find a clever way
  while(TRUE){
    if((x[it] > threshold)==TRUE){
      if (norm){
        x[it] <- 1
      }
      x[(it+1):(it+nsamples.ignore)] <- 0
      it <- it + nsamples.ignore
    }else{
      x[it] <- 0
      it <- it + 1
    }
    if (it > N) return(x)
  } 
}


calc.bpm <- function(peaks, fs){
  diff.peaks <- diff(which(peaks==1))
  bpm <- 1/diff.peaks*fs*60
}


#' ggplot2 theme from minimaxir.com
#'
#' @param scale_text use to scale the size of the text
#' @param font Well, the font you want
#' @examples
#'  ggplot(data=data.frame(x=1:100, y=rnorm(100)),aes(x=x,y=y))+
#'  geom_point()+labs(title="rnd", x="x",y="y")+theme_mini(scale_text=1.5)

theme_mini <- function(scale_text=1, font="Impact") {
  
  
  
  # best font = "Impact", Times New Roman, Helvetica, Garamond, Futura, Lowetica
  # NEW BEST = "Arial Black", "Comfortaa", "Impact"
  # Generate the colors for the chart procedurally with RColorBrewer
  
  # Credit: Max Woolf http://minimaxir.com
  
  library(RColorBrewer)
  library(grid)
  palette <- brewer.pal("Greys", n=9)
  color.background = palette[1]
  color.grid.major = palette[3]
  color.axis.text = palette[6]
  color.axis.title = palette[7]
  color.title = palette[9]
  
  # Begin construction of chart
  theme_bw(base_size=9) +
    
    # Set the entire chart region to a light gray color
    theme(text=element_text(family=font))+
    theme(panel.background=element_rect(fill=color.background, color=color.background)) +
    theme(plot.background=element_rect(fill=color.background, color=color.background)) +
    theme(panel.border=element_rect(color=color.background)) +
    
    # Format the grid
    theme(panel.grid.major=element_line(color=color.grid.major,size=.25)) +
    theme(panel.grid.minor=element_blank()) +
    theme(axis.ticks=element_blank()) +
    
    # Format the legend, but hide by default
    #theme(legend.position="none") +
    theme(legend.background = element_rect(fill=color.background)) +
    theme(legend.text = element_text(size=7*scale_text,color=color.axis.title)) +
    
    # Set title and axis labels, and format these and tick marks
    theme(plot.title=element_text(color=color.title, size=10*scale_text, vjust=1.25)) +
    theme(axis.text.x=element_text(size=7*scale_text,color=color.axis.text)) +
    theme(axis.text.y=element_text(size=7*scale_text,color=color.axis.text)) +
    theme(axis.title.x=element_text(size=8*scale_text,color=color.axis.title, vjust=0)) +
    theme(axis.title.y=element_text(size=8*scale_text,color=color.axis.title, vjust=1.25)) +
    
    # Plot margins
    theme(plot.margin = unit(c(0.35, 0.2, 0.3, 0.35), "cm"))
}