ggplot for glmnet

ggplot.coefs.R

plotCoefs = function(model, nonzero = T, subset.condition, ...) {
  stopifnot(require(ggplot2))
  coefs = coef(model)[,1]
  coef.labels = attr(coefs, "names")
  
  isLogistic = model$name == "Binomial Deviance"
  if (isLogistic) coefs = exp(coefs)
  coefs.df = data.frame(label = coef.labels, value = coefs)
  coefs.df = coefs.df[order(coefs.df$value),]
  coefs.df$label = factor(coefs.df$label, levels = coefs.df$label)
  
  coefs.df = subset(coefs.df, label != "(Intercept)")
  if (nonzero) coefs.df = droplevels(subset(coefs.df, value != ifelse(isLogistic, 1, 0)))
  if (!missing(subset.condition)) coefs.df = droplevels(subset(coefs.df, eval(subset.condition, coefs.df)))
  
  if (isLogistic) {
    coefs.df$sign = ">1"
    coefs.df$sign[which(coefs.df$value == 1)] = "=1"
    coefs.df$sign[which(coefs.df$value < 1)] = "<1"
    coefs.df$sign = factor(coefs.df$sign, levels = c("<1", "=1", ">1"))
  } else {
    coefs.df$sign = ">0"
    coefs.df$sign[which(coefs.df$value == 0)] = "=0"
    coefs.df$sign[which(coefs.df$value < 0)] = "<0"
    coefs.df$sign = factor(coefs.df$sign, levels = c("<0", "=0", ">0"))
  }
  
  p = ggplot(coefs.df,aes(x = label, y = value, fill = sign))
  p +
    geom_bar(stat='identity') +
    coord_flip() +
    theme_grey(base_size = 25) + 
    xlab("Variable") + ylab(ifelse(isLogistic, "Odds Ratio Multiplier", "Value"))
}

plotFactorCoefs = function(model, variable, ...) {
  stopifnot(require(ggplot2))
  variable.ch = deparse(substitute(variable))
  coefs = coef(model)[,1]
  coef.labels = attr(coefs, "names")
  variable.levels = levels(eval(substitute(variable), model$data))
  #variable.indices = grep(paste("^",variable.ch, ".*", sep=""), coef.labels)
  variable.indices = which(coef.labels %in% paste(variable.ch, variable.levels, sep=""))
  
  base = paste(variable.ch, variable.levels[1], sep="")
  labels = c(coef.labels[variable.indices], base)
  values = c(coefs[variable.indices], 0)
  isLogistic = model$name == "Binomial Deviance"
  if (isLogistic) values = exp(values)
  coefs.df = data.frame(label = labels, value = values)
  n = nrow(coefs.df)
  coefs.df[1:(n-1),] = coefs.df[1:(n-1),][order(coefs.df$value[1:(n-1)], coefs.df$label[1:(n-1)]),]
  coefs.df$label = factor(coefs.df$label, levels = coefs.df$label)
  
  if (isLogistic) {
    coefs.df$sign = ">1"
    coefs.df$sign[which(coefs.df$value == 1)] = "=1"
    coefs.df$sign[which(coefs.df$value < 1)] = "<1"
    coefs.df$sign = factor(coefs.df$sign, levels = c("<1", "=1", ">1"))
  } else {
    coefs.df$sign = ">0"
    coefs.df$sign[which(coefs.df$value == 0)] = "=0"
    coefs.df$sign[which(coefs.df$value < 0)] = "<0"
    coefs.df$sign = factor(coefs.df$sign, levels = c("<0", "=0", ">0"))
  }
  
  p = ggplot(coefs.df,aes(x = label, y = value, fill = sign))
  p +
    geom_bar(stat='identity') +
    coord_flip() +
    theme_grey(base_size = 25) + 
    xlab(variable.ch) + ylab(ifelse(isLogistic, "Odds Ratio Multiplier", "Value")) + labs(title = variable.ch)
}