[R] Help reproducing this boxplot

[Ryan Treacy]

I am trying to reproduce the style of boxplot pictured in the attached
image.  The code below is close but I cannot get the control values the
correct color.

library(ggplot2)

box.print <- function(C1M,C1, D2, QCDC2, QCSDT4, num){
  NAME <- names(D2[num])
  adjsdt4 <- C1M[,num]
  sdt4 <- C1[,num]
  disco2 <- D2[,num]
  qcdc <- QCDC2[,num]
  qcsdt4 <- QCSDT4[,num]
  adj <- data.frame(Intensity=c(adjsdt4,qcsdt4),
                    Study= rep("adjSDT4",length(adjsdt4)+length(qcsdt4)),
                    QC=
c(rep("cases",length(adjsdt4)),rep("QC",length(qcsdt4)))

  )
  nadj <- data.frame(Intensity=c(sdt4,qcsdt4),
                     Study= rep("SDT4",length(sdt4)+length(qcsdt4)),
                     QC=
c(rep("cases",length(sdt4)),rep("QC",length(qcsdt4)))

  )
  disco <- data.frame(Intensity=c(disco2,qcdc),
                      Study= rep("DISCO2",length(disco2)+length(qcdc)),
                      QC=
c(rep("cases",length(disco2)),rep("QC",length(qcdc)))

  )
  full <- rbind(adj,nadj,disco)

  g1 <- ggplot(full, aes(x=Study, y=Intensity))+geom_boxplot(outlier.shape
= NA)+ggtitle(NAME)+
    geom_jitter(alpha=0.5, aes(color=Study,label=Study,shape=QC),position =
position_jitter(width = .8),size=2)
  g1 = g1+theme(panel.grid.major= element_blank(),
                panel.grid.minor= element_blank(),
                panel.background= element_blank(),
                panel.border= element_rect(colour="black",fill=NA),
                legend.position="none")
  g1= g1+scale_shape_manual(values=c(19,1))+scale_fill_discrete(guide=FALSE)
  print(g1)
}

A <- data.frame(1.557, 1.663, 1.637, 1.740, 1.597, 1.473, 1.399 ,1.403,
1.210, 1.375, 1.387, 1.515, 1.456,
  1.121, 1.211, 1.165, 1.428, 1.749, 1.231, 1.209, 1.272, 1.580, 1.254,
1.099, 1.151, 1.239,
  1.753, 1.415, 1.653, 1.555, 1.748, 1.951, 1.734, 1.519, 1.397, 1.391,
1.825, 1.722, 1.715,
  1.777, 2.014, 1.676, 1.803, 1.332, 1.560, 1.605, 1.564, 1.588, 1.583,
1.701, 1.297, 1.583,
  1.778, 1.343, 1.427, 1.472, 1.663, 1.472, 1.726, 1.327, 1.466, 1.890,
1.601, 1.474, 1.671,
  1.492, 1.277, 1.524, 1.394, 1.477, 1.525, 1.502, 1.371, 1.479, 0.966,
1.239, 1.415, 1.316,
  1.336, 1.244, 2.040, 1.823, 1.853, 1.712, 1.805, 1.593, 1.630, 1.578,
1.648, 1.581, 1.661,
  1.731, 1.360, 1.572, 1.788, 1.668, 1.663, 1.519)
A <- t(A)
B <- A*.3
C <- A*2
QA <- data.frame(1.951, 1.734, 1.519, 1.397, 1.391, 1.825)
QA <- t(QA)
QC <- QA*1.5

box.print(A,B,C,QA,QC,1)
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