rggplot2regressionquantilevgam

Percentiles from VGAM


I am using following example from help pages of package VGAM

library(VGAM)
fit4 <- vgam(BMI ~ s(age, df = c(4, 2)), lms.bcn(zero = 1), data = bmi.nz, trace = TRUE)
qtplot(fit4, percentiles = c(5,50,90,99), main = "Quantiles", las = 1, xlim = c(15, 90), ylab = "BMI", lwd = 2, lcol = 4) 

I am getting a proper graph with it:

enter image description here

How can I avoid plotting points from the graph? Also I need to print out values for these percentiles at each of ages 20,30,40...80 (separately as a table). How can this be done? Can I use ggplot() format command rather than qtplot() command here? Thanks for your help.


Solution

  • How about something like this:

    # required packages
    library(VGAM)
    require(reshape2)
    require(ggplot2)
    # fitted values from vgam 
    fit4 <- vgam(BMI ~ s(age, df = c(4, 2)), lms.bcn(zero = 1), data = bmi.nz, trace = TRUE)
    fitted.values <- data.frame(qtplot.lmscreg(fit4, percentiles = c(5,50,90,99))$fitted.values)
    fitted.values[, 'age'] <- bmi.nz[, 'age']
    # melt data.frame
    dmelt <- melt(fitted.values, id.vars='age')
    # ploting
    ggplot(dmelt, aes(age, value, group=variable)) + 
      geom_line(color='blue') + 
      annotate(geom='text', 
               x = max(bmi.nz[, 'age']) + 3, 
               y = unlist(fitted.values[which.max(fitted.values[, 'age']), -ncol(fitted.values)]),
               label=c(' 5%', '50%', '90%', '99%')) +
      lapply(2:8*10, function(i) {
        annotate(geom='text', 
               x = i, 
               y = 1+unlist(fitted.values[which.min(abs(fitted.values[, 'age'] - i)), -ncol(fitted.values)]),
               label=paste0(round(unlist(fitted.values[which.min(abs(fitted.values[, 'age'] - i)), -ncol(fitted.values)]),1), '%'))
      }) +
      scale_y_continuous('BMI') +
      theme_bw(base_size=16)