R/calculateCoordinates.R

In sp00nman/evoplot: A small package to draw clonal evolution plots

#' Calculate gamma coordinates to draw the polygons
#' 
#'              (beta)
#'              ^ 
#'            + + 
#'  (gamma) < + + 
#'            + + 
#'              v 
#'              (alpha)
#'
#'@param freq_clones A vector with the frequency of the clones \code{freq_clones}
#'@param xaxis_length Length of the x-axis \code{xaxis_length}
#'@param yaxis_length Length of the y-axis \code{yaxis_length}
#'@param xy_start Coordinates for the starting point of the plot \code{xy_start}
#'
#'@return dataframe Returns a dataframe with x and y coordinates for point gamma
#'
#'@keywords coordinates gamma alpha beta
#'
#'@export
#'
#'@examples
#'alpha_beta <- calculate.alpha.beta.coordinates(df[df$clone==1, ],
#'                                               xaxis_length=4,
#'                                               yaxis_length=yaxis_length_per_clone[1],
#'                                               xy_start=c(0,0))
calculate.gamma.coordinates <- function(freq_clones, xaxis_length, 
                                        yaxis_length, xy_start=c(0,0),
                                        debug=FALSE) {
  offset <- xy_start[2] #length of the clone
  y_coord <- (yaxis_length/2)+offset
  num_clones <- length(freq_clones$clone)
  
  if (debug) {print(c("yaxis_length: ", yaxis_length))}
  if (debug) {print(c("offset: ", offset))}
  if (debug) {print(c("y_coord: ", y_coord))}
  if (debug) {print(c("number of clones: ", num_clones))}
  if (debug) {print(c("x-axis_length: ", xaxis_length))}
  
  x <- c()
  y <- rep(y_coord,num_clones)
  
  if (debug) {print(c("y: ",y))}
  
  x_gamma_start <- xy_start[1] #draw first point [1] -->x
  dis_points <- (xaxis_length*(9/10)/num_clones)
  
  if (debug) {print(c("dis_points: ", dis_points))}
  
  x <- cbind(x, x_gamma_start)
  num_polygons <- length(freq_clones$clone)
  if (debug) {print(c("nr_triangles: ", num_polygons))}
  j=1
  if (num_polygons!=1){     
    for (i in 1:(num_polygons-1)) {  #-1 --> x[1] is filled with x_gamma_start
      if (debug) {print(c("j: ", j))}
      if (debug) {print(c("x[j]: ", x[j]))}
      
      x <- cbind(x, x[j]+dis_points)
      j=j+1
      
      if (debug) {print(c("x", x))}
    }
  }
  return(data.frame(x=as.vector(x), y=as.vector(y)))
}

#' Calculate alpha & beta coordinates to draw the polygons
#' 
#'              (beta)
#'              ^ 
#'            + + 
#'  (gamma) < + + 
#'            + + 
#'              v 
#'              (alpha)
#'
#'@param freq_clones A vector with the frequency of the clones \code{freq_clones}
#'@param xaxis_length Length of the x-axis \code{xaxis_length}
#'@param yaxis_length Length of the y-axis \code{yaxis_length}
#'@param xy_start Coordinates for the starting point of the plot \code{xy_start}
#'
#'@return dataframe Returns a dataframe with x and y coordinates for alpha & beta
#'
#'@keywords coordinates alpha beta
#'
#'@export
#'
#'@examples
#'alpha_beta <- calculate.alpha.beta.coordinates(df_freq[df_freq$clone==1, ],
#'                                               xaxis_length=4,
#'                                               yaxis_length=yaxis_length_per_clone[1],
#'                                               xy_start=c(0,0),
#'                                               debug=TRUE)
calculate.alpha.beta.coordinates <- function(freq_clones, xaxis_length, 
                                             yaxis_length, xy_start=c(0,0),
                                             debug=FALSE){
  offset <- xy_start[2] #where to place the polygon
  y_coord <- (yaxis_length/2)+offset
  nr_clones <- length(freq_clones$clone)
  
  if (debug) {print(c("offset: ", offset))}
  if (debug) {print(c("yaxis_length: ", yaxis_length))}
  if (debug) {print(c("y_coord: ", y_coord))}
  if (debug) {print(c("number of clones: ", nr_clones))}
  if (debug) {print(c("freq_length: ", xaxis_length))}
  
  x <- rep(xaxis_length, nr_clones)
  
  if (debug) {print(c("x:", x))}
  
  y_alpha <- c()
  y_alpha_a <- c()
  y_beta <- c()
  y_beta_a <- c()
  rel_dis <- c()
  prev_rel_dis <- 0
  rel_clones <- c()

  for (i in 1:nr_clones){
    if (debug) {print(c("i: ", i))}
    
    rev_clones <- rev(as.character(freq_clones$subclone)) #order C-->B-->A
    rel_dis <- cbind(rel_dis, ((xaxis_length*freq_clones[freq_clones$subclone==rev_clones[i], ]$subclone_freq)/100))
    
    if (debug) {print(c("subclone: ", rev_clones[i]))}
    if (debug) {print(c("rel_dis: ", rel_dis))}
    if (debug) {print(c("prev_rel_dis:", prev_rel_dis))}
    
    y_alpha <- cbind(y_alpha, y_coord - ((rel_dis[i]/2)  + (prev_rel_dis/2)))
    y_beta <- cbind(y_beta, y_coord + ((rel_dis[i]/2) + (prev_rel_dis/2)))
    y_alpha <- rev(y_alpha)
    y_beta <- rev(y_beta)
    
    prev_rel_dis <- rel_dis[i]
    
    if (debug) {print(c("y_alpha:", y_alpha))}
    if (debug) {print(c("y_beta:", y_beta))}
  }
  
  return(data.frame(x=as.vector(x), 
                    y_alpha=as.vector(y_alpha), 
                    y_beta=as.vector(y_beta)))
}