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Kernel: R (R-Project)
require(ggplot2)
p1 <- ggplot(mpg, aes(x=class, y=hwy)) +
    geom_boxplot(color="blue", fill="blue", alpha=0.2, notch=TRUE, notchwidth = 0.8,
        outlier.colour="red", outlier.fill="red", outlier.size=3
    )

p1
Loading required package: ggplot2 notch went outside hinges. Try setting notch=FALSE. notch went outside hinges. Try setting notch=FALSE.
Image in a Jupyter notebook

… saving plot to PDF

pdf("r-cars-plot.pdf")
p1
dev.off()
notch went outside hinges. Try setting notch=FALSE. notch went outside hinges. Try setting notch=FALSE. 
require("fishmethods")
Loading required package: fishmethods Loading required package: MASS Loading required package: boot Loading required package: bootstrap Loading required package: lme4 Loading required package: Matrix Loading required package: numDeriv 
data(rig)
fit <- grotagplus(rig,dataID="Sex",alpha=70,beta=100,
                  model=list(mean="Francis",var="linear",seas="none"),
                 design=list(galpha=list("F","M"),gbeta=list("F","M"),
                             s=1,nu=1,m=0,p=0),
                  stvalue=list(galpha=c(5,4),gbeta=c(3,2),s=2,nu=0.5),
                  upper=list(galpha=c(8,6),gbeta=c(5,4),s=4,nu=1),
                 lower=list(galpha=c(3,2),gbeta=c(1.5,1),s=0.5,nu=0.2))
mnlenatage <- list(F=90.7*(1-exp(-0.42*(seq(1.5,6.5)-0.77))),
           M= 118.7*(1-exp(-0.16*(seq(4,11)-2.02))),
           PGM=161.1*(1-exp(-0.11*(seq(3.5,10.5)-1.91))))
plot(fit,age.based.growth=mnlenatage)
## Residual plots
fit <- grotagplus(rig,dataID="Sex",alpha=70,beta=100,
                  model=list(mean="Francis",var="linear",seas="none"),
                 design=list(galpha=list("F","M"),gbeta=list("F","M"),
                             s=1,nu=1,m=0,p=0),
                  stvalue=list(galpha=c(5,4),gbeta=c(3,2),s=2,nu=0.5),
                  upper=list(galpha=c(8,6),gbeta=c(5,4),s=4,nu=1),
                 lower=list(galpha=c(3,2),gbeta=c(1.5,1),s=0.5,nu=0.2))
plot(fit,"resid")
plot(fit,"resid",resid.spec=list(Pearson=FALSE,x="L1"))
## Trajectory plot as in Fig. 2 of Francis (1988)
data(bonito)
fit <- grotagplus(bonito,alpha=35,beta=55,
               design=list(galpha=1,gbeta=1,s=1,nu=1,m=1,p=1,u=1,w=1),
               stvalue=list(s=0.81,nu=0.3,m=0,p=0.01,u=0.5,w=0.5),
               upper=list(s=3,nu=1,m=2,p=0.1,u=1,w=1),
               lower=list(s=0.1,nu=0.1,m=-2,p=0,u=0,w=0))
plot(fit,"traj",Linitial=35)
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3D plot package

library("plot3D")
with(USArrests, text3D(Murder, Assault, Rape, 
  labels = rownames(USArrests), colvar = UrbanPop, 
  col = gg.col(100), theta = 60, phi = 20,
  xlab = "Murder", ylab = "Assault", zlab = "Rape", 
  main = "USA arrests", cex = 0.5, 
  bty = "g", ticktype = "detailed", d = 3,
  clab = c("Urban","Pop"), adj = 0.5, font = 2))
# Add points
 with(USArrests, scatter3D(Murder, Assault, Rape - 1, 
    colvar = UrbanPop, col = gg.col(100), 
    type = "h", pch = ".", add = TRUE))
Image in a Jupyter notebook