daDoctoR/R/plot_ord_odds.R
agdamsbo a0c01207b8 u
2018-10-10 09:47:46 +02:00

47 lines
1.4 KiB
R

#' Forrest plot from ordinal logistic regression
#'
#' Heavily inspired by https://www.r-bloggers.com/plotting-odds-ratios-aka-a-forrestplot-with-ggplot2/
#' @param x ordinal logistic regression model.
#' @param title plot title
#' @param dec decimals for labels
#' @param lbls labels for variable names. Carefull, as the right order is not checked automatically!
#' @param short flag to half number of ticks on horizontal axis.
#' @keywords forestplot
#' @export
#' @examples
#' plot_ord_odds()
plot_ord_odds<-function(x, title = NULL,dec=3,lbls=NULL,short=FALSE){
require(ggplot2)
odds<-data.frame(cbind(exp(coef(x)), exp(confint(x))))
names(odds)<-c("or", "lo", "up")
rodds<-round(odds,digits = dec)
if (!is.null(lbls)){
odds$vars<-paste0(lbls," \n",paste0(rodds$or," [",rodds$lo,":",rodds$up,"]"))
}
else {
odds$vars<-paste0(row.names(odds)," \n",paste0(rodds$or," [",rodds$lo,":",rodds$up,"]"))
}
ticks<-c(seq(0, 1, by =.1), seq(0, 10, by =1), seq(10, 100, by =10))
if (short==TRUE){
ticks<-ticks[seq(1, length(ticks), 2)]
}
else {ticks<-ticks}
odds$ord<-c(nrow(odds):1)
ggplot(odds, aes(y= or, x = reorder(vars,ord))) +
geom_point() +
geom_errorbar(aes(ymin=lo, ymax=up), width=.2) +
scale_y_log10(breaks=ticks, labels = ticks) +
geom_hline(yintercept = 1, linetype=2) +
coord_flip() +
labs(title = title, x = "Variables", y = "OR (95 % CI)") +
theme_bw()
}