R/ggLogReg.R

In cardiomoon/moonBook2: Functions and Datasets for the 2nd Book by Keon-Woong Moon

require(ggplot2)
require(ggiraph)

#' Draw a jittered scatter plot for logistic regression model
#'@param data a data.frame
#'@param yvar A character string of column name be used as a response(y-axis) variable.
#'@param xvar A character string of column name be used as a explanatory(x-axis) variable
#'@param se Logical. display confidence interval around linear regression? (TRUE by default)
#'@param interactive A logical value. If TRUE, an interactive plot will be returned
#'@param ... other arguments passed on to geom_point


ggLogReg=function(data,yvar,xvar,se=TRUE,interactive=FALSE,digits=2,...){
    data$id=1:nrow(data)
    data$tooltip=paste0(data$id,"<br>",xvar,"=",data[[xvar]],"<br>",yvar,"=",data[[yvar]])

    fit=glm(as.formula(paste0(yvar,"~",xvar)),data=data,family=binomial)
    b0=coef(fit)[1]
    b1=coef(fit)[2]
    f=function(x) 1/(1+exp(-(b1*x+b0)))

    x=seq(min(data[[xvar]],na.rm=T),max(data[[xvar]],na.rm=T),length.out=100)
    y=f(x)
    tooltip=paste0("y=1/(1+exp(-(",round(b1,digits),"x",ifelse(b0>=0,"+","-"),abs(round(b0,digits)),")))")
    df1=data.frame(x,y,id="1",tooltip=tooltip)

    p<-ggplot(data,aes_string(x=xvar,y=yvar))+
        stat_smooth(method='glm',method.args=list(family='binomial'),se=se,colour=NA)+
        geom_point_interactive(aes(tooltip=tooltip,data_id=id),
                               position=position_jitter(width=0.3,height=0.06),alpha=0.5,...)+
        geom_path_interactive(data=df1,aes(x=x,y=y,tooltip=tooltip,data_id=id),colour="blue",size=1)

    if(interactive){
        tooltip_css <- "background-color:white;font-style:italic;padding:10px;border-radius:10px 20px 10px 20px;"
        #hover_css="fill-opacity=.3;cursor:pointer;stroke:gold;"
        hover_css="r:4px;cursor:pointer;stroke-width:6px;"
        selected_css = "fill:#FF3333;stroke:black;"
        p<-ggiraph(code=print(p),tooltip_extra_css=tooltip_css,tooltip_opacity=.75,
                   zoom_max=10,hover_css=hover_css,selected_css=selected_css)
    }
    p

}