R/plot_odds.R

In jomuller/ITCARES: an Interactive Tool for Case-crossover Analyses of electronic medical REcords for patient Safety

plot_odds<-function(x, title = NULL){
  require(ggplot2)
  odds <-data.frame(cbind(exp(coef(x)), exp(confint(x))))
  #     odds<-tmp[-1,]
  names(odds)<-c('OR', 'lower', 'upper')
  odds$vars<-ordered(row.names(odds), levels = row.names(odds))
  odds$vars <- gsub(pattern = 'latency', replacement = '', x = odds$vars)
  odds$vars<-ordered(odds$vars, levels = odds$vars)
  
  ggplot(odds, aes(y= OR, x = vars)) +
    geom_point(size = 3) + 
    geom_errorbar(aes(ymin=lower, ymax=upper), width=0, size = 1) +
    scale_y_continuous(breaks=seq(0, max(odds$upper, na.rm = TRUE)+2, 1)) +
    geom_hline(yintercept = 1, linetype=2, size = 1) +
    expand_limits(y=.8) +
    labs(x = 'Days after exposure', y = 'Odds ratio for primary outcome') + 
    theme_classic() +
    theme(axis.title.x = element_text(size = 16, face="bold",margin=margin(20,0,0,0)),
          axis.title.y = element_text(size = 16, face="bold",margin=margin(0,20,0,0)),
          axis.text.x = element_text(lineheight=.8,size = 12, vjust=0.5),
          axis.text.y = element_text(lineheight=.8,size = 12),
          axis.line.x = element_line(colour = 'black', size=0.5, linetype='solid'),
          axis.line.y = element_line(colour = 'black', size=0.5, linetype='solid')    
    )
}