mirror of
https://github.com/agdamsbo/daDoctoR.git
synced 2024-11-24 12:41:54 +01:00
54 lines
1.8 KiB
R
54 lines
1.8 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 input data.
|
|
#' @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 hori labels the horizontal axis (this i the y axis as the plot is rotated)
|
|
#' @param vert labels the horizontal axis (this i the x axis as the plot is rotated)
|
|
#' @param short flag to half number of ticks on horizontal axis.
|
|
#' @param input can be either "model", which is a olr model (polr()), or "df", which is a dataframe whith three columns for OR, lower CI and upper CI-
|
|
#' @keywords forestplot
|
|
#' @export
|
|
|
|
plot_ord_odds<-function(x, title = NULL,dec=3,lbls=NULL,hori="OR (95 % CI)",vert="Variables",short=FALSE,input="model"){
|
|
|
|
require(ggplot2)
|
|
|
|
if (input=="model"){
|
|
odds<-data.frame(cbind(exp(coef(x)), exp(confint(x))))
|
|
}
|
|
|
|
if (input=="df"){
|
|
odds<-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(1, 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 = vert, y = hori) +
|
|
theme_bw()
|
|
}
|