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64 lines
2.2 KiB
R
64 lines
2.2 KiB
R
utils::globalVariables(c("or","ord","lo","up"))
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#' Forest plot from ordinal logistic regression.
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#'
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#' Heavily inspired by https://www.r-bloggers.com/plotting-odds-ratios-aka-a-forrestplot-with-ggplot2/
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#'
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#' @param x input data.
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#' @param title plot title
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#' @param dec decimals for labels
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#' @param lbls labels for variable names. Careful, as the right order is not checked automatically!
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#' @param hori labels the horizontal axis (this i the y axis as the plot is rotated)
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#' @param vert labels the horizontal axis (this i the x axis as the plot is rotated)
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#' @param short flag to half number of ticks on horizontal axis.
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#' @param input can be either "model", which is a olr model (polr()), or "df", which is a data frame with three columns for OR, lower CI and upper CI.
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#'
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#' @return gg object
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#' @keywords forest plot
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#'
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#' @import ggplot2 stats MASS
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#'
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#' @export
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#'
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#' @examples
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#' iris$ord<-factor(sample(1:3,size=nrow(iris),replace=TRUE),ordered=TRUE)
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#' lm <- MASS::polr(ord~., data=iris, Hess=TRUE, method="logistic")
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#' plot_olr(lm, input="model")
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plot_olr<-function(x, title = NULL, dec=3, lbls=NULL, hori="OR (95 % CI)", vert="Variables", short=FALSE, input=c("model","df")){
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if (input=="model"){
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odds <- data.frame(cbind(exp(coef(x)), exp(confint(x))))
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}
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if (input=="df"){
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odds <- x
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}
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names(odds)<-c("or", "lo", "up")
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rodds<-round(odds, digits = dec)
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if (!is.null(lbls)){
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odds$vars<-paste0(lbls," \n",paste0(rodds$or," [",rodds$lo,":",rodds$up,"]"))
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} else {
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odds$vars<-paste0(row.names(odds)," \n",paste0(rodds$or," [",rodds$lo,":",rodds$up,"]"))
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}
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ticks<-c(seq(0, 1, by =.1), seq(1, 10, by =1), seq(10, 100, by =10))
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if (short==TRUE){
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ticks<-ticks[seq(1, length(ticks), 2)]
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}
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odds$ord<-c(nrow(odds):1)
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odds|>
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ggplot2::ggplot(mapping = ggplot2::aes(y = or, x = reorder(vars,ord))) +
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ggplot2::geom_point() +
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ggplot2::geom_errorbar(mapping = ggplot2::aes(ymin=lo, ymax=up), width=.2) +
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ggplot2::scale_y_log10(breaks=ticks, labels = ticks) +
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ggplot2::geom_hline(yintercept = 1, linetype=2) +
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ggplot2::coord_flip() +
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ggplot2::labs(title = title, x = vert, y = hori) +
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ggplot2::theme_bw(14)
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}
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