R/similarity_map.R

In michaelgavin/litmath: Literary Mathematics

#' Create a semantic map of a keyword
#' 
#' Build a scatterplot that represents the conceptual structure of a keyword.
#' 
#' @param mat A word-context matrix.
#' 
#' @param keyword A string.
#' 
#' @param method A character string: 'cosine', 'euclidean', 'pearson' or 'covariance', which names
#'              the mathematical similarity test to be performed. Default is 'cosine'.
#' 
#' @param margin Numeric value: 1 or 2. If 1, calculations are performed over the rows. If 2, over
#'              the columns.
#' 
#' @param numResults Numeric value. The number of words to be displayed in the 
#'                   graph. Default is 40.
#'  
#' @param numGrps Numeric value. The number of groups in which you'd like to divide
#'                the display. Default is 5.
#'       
#' @return A scatterplot showing structure of 30 most-similar words.
#' 
#' @section What it does:
#' This function runs \code{\link{most_similar}} over a word-context matrix and looks for the
#' thirty most similar terms, then clusters them.
#' @export
similarity_map = function(mat, 
                          keyword, 
                          method = "cosine", 
                          margin = 1,
                          numResults = 40, 
                          numGrps = 5) {

  if (method %in% c("cosine", "euclidean", "pearson", "covariance") == F) {
    stop("The 'method' argument must be deployed: 'cosine', 'euclidean', 'pearson', 'covariance'.")
  }
  
  # Get words most similar to keyword
  results = most_similar(mat = mat, vec = keyword, method = method, margin = margin, fullResults = T)
  if (method == "euclidean") {
    results = sort(results)[1:numResults]
  } else {
    results = sort(results, decreasing = T)[1:numResults]
  }
  words = names(results)
  
  # Set correlation method
  
  if (method == "cosine") {
    corr_method = function(x, y) { x %*% y/(sqrt(x %*% x) * sqrt(y %*% y)) }
  } 
  if (method == "euclidean") {
    corr_method = function(x, y) { sqrt(sum((x - y)^2)) }
  }
  if (method == "covariance") {
    corr_method = cov
  }
  if (method == "pearson") {
    corr_method = cor
  }
  
  # Now build a correlations matrix among the words
  if (margin == 1) {
    mat = mat[words, ]
    correlations = matrix(0, length(words), length(words))
    for (i in 1:nrow(correlations)) {
      correlations[i, ] = apply(mat, 1, corr_method, mat[i, ])
    }
    rownames(correlations) = words
    
    hc = hclust(dist(correlations))
    cluster <- cutree(hc, k=numGrps)
    xy <- data.frame(cmdscale(dist(correlations)), factor(cluster), factor(words))
    names(xy) <- c("x", "y", "clusts", "words")
    
    single_item_cluster = which(table(xy$clusts) == 1)
    bad_hits = which(xy$clusts %in% single_item_cluster)
    
    outliers = c()
    if (any(bad_hits)) {
      outliers = xy$words[bad_hits]
      xy = xy[-bad_hits,]
    }
    
    xdiff = (max(xy$x) - min(xy$x)) / 4
    ydiff = (max(xy$y) - min(xy$y)) / 4
    p = ggplot(xy, aes(x, y, label = words, group = clusts))
    if (length(outliers) == 0) {
      p = p + xlab("") 
    }
    if (length(outliers) == 1) {
      p = p + xlab(paste("Outlier excluded from graph:", paste(outliers, collapse = ", "))) 
    }
    if (length(outliers) > 1) {
      p = p + xlab(paste("Outliers excluded from graph:", paste(outliers, collapse = ", "))) 
    } 
    p = p + stat_density2d(aes(alpha = ..level.., fill = clusts), geom="polygon", bins = 30, size = 0) + 
      scale_alpha_continuous(range=c(0.01,0.033)) +
      geom_text(colour = "black") +
      theme_bw() +
      xlim(min(xy$x) - xdiff, max(xy$x) + xdiff) +
      ylim(min(xy$y) - ydiff, max(xy$y) + ydiff) +
      ylab("") +
      theme(axis.line = element_line(colour = "black"),
            panel.grid.major = element_blank(),
            panel.grid.minor = element_blank(),
            panel.border = element_blank(),
            axis.ticks = element_blank(),
            axis.line.x = element_blank(),
            axis.line.y = element_blank(),
            legend.position = 'none',
            text = element_text(size = 2),
            title = element_text(size=10, face='bold'))
    print(p)
  }
  if (margin == 2) {
    mat = mat[,words]
    correlations = matrix(0, length(words), length(words))
    for (i in 1:nrow(correlations)) {
      correlations[, i] = apply(mat, 2, corr_method, mat[, i])
    }
    rownames(correlations) = words
    
    hc = hclust(dist(correlations))
    cluster <- cutree(hc, k=numGrps)
    
    data(tcp)
    row.names(tcp) = tcp$TCP
    titles = tcp[words,"Title"]
    titles = substring(titles, 1, 20)
    titles = paste(words, titles, sep=", ")
    xy <- data.frame(cmdscale(dist(correlations)), factor(cluster), titles)
    names(xy) <- c("x", "y", "clusts", "words")
    
    single_item_cluster = which(table(xy$clusts) == 1)
    bad_hits = which(xy$clusts %in% single_item_cluster)
    
    outliers = c()
    if (any(bad_hits)) {
      outliers = xy$words[bad_hits]
      xy = xy[-bad_hits,]
    }
    
    xdiff = (max(xy$x) - min(xy$x)) / 4
    ydiff = (max(xy$y) - min(xy$y)) / 4
    
    p = ggplot(xy, aes(x, y, label = words, group = clusts))
    if (length(outliers) == 0) {
      p = p + xlab("") 
    }
    if (length(outliers) == 1) {
      p = p + xlab(paste("Outlier excluded from graph:", paste(outliers, collapse = ", "))) 
    }
    if (length(outliers) > 1) {
      p = p + xlab(paste("Outliers excluded from graph:", paste(outliers, collapse = ", "))) 
    } 
    p = p + stat_density2d(aes(alpha = ..level.., fill = clusts), geom="polygon", bins = 30, size = 0) + 
      scale_alpha_continuous(range=c(0.01,0.033)) +
      geom_text(colour = "black") +
      theme_bw() +
      xlim(min(xy$x) - xdiff, max(xy$x) + xdiff) +
      ylim(min(xy$y) - ydiff, max(xy$y) + ydiff) +
      ylab("") +
      theme(axis.line = element_line(colour = "black"),
            panel.grid.major = element_blank(),
            panel.grid.minor = element_blank(),
            panel.border = element_blank(),
            axis.ticks = element_blank(),
            axis.line.x = element_blank(),
            axis.line.y = element_blank(),
            legend.position = 'none',
            text = element_text(size = 2),
            title = element_text(size=10, face='bold'))
    print(p)
  }
 
    
}