# Chris Hamm on using plot.new() for better combined plots

by Noam Ross, 26 October 2012

At DRUG today, Chris Hamm (email) showed us an easier way to combine multiple figures into one plot using plot.new, rather than par(mfrow=...) Here’s his script:

A Report Generated by knitr
# plot.new() cahamm@ucdavis.edu

#I discovered this plotting method when trying to add an inset figure
# to a plot

# plot.new is part of the traditional graphics. This function starts a new plot with the
# scale of the x- and y- axes to (0,1) This allows you to specify the location of each
# pane or inset and provides a high level of customizability for R graphics

############### Plotting multiple panes, the old way
par(mfrow = c(3, 1))

plot(P2B1$TMP, ylab = "Degrees C", xlab = "3 January - 13 March, 2011", type = "l", lty = 1, ylim = c(-25, 15), xaxt = "n", lwd = 2) lines(P2T1$TMP, type = "l", lty = 2, col = "red", lwd = 2)
# line at DD50 (10C = 50F)
legend("topleft", legend = c("Ground Level", "1m Height"), col = c("black", "red"), lty = c(1,
2), lwd = c(2, 2), bty = "n")

plot(P2B2$TMP, ylab = "Degrees C", xlab = "13 March - 7 May, 2011", type = "l", lty = 1, lwd = 2, ylim = c(-10, 35), xaxt = "n") lines(P2T2$TMP, col = "red", lwd = 2, lty = 2)

plot(P2B3$TMP, ylab = "Degrees C", xlab = "7 May - 16 July, 2011", type = "l", ylim = c(0, 38), xaxt = "n", lwd = 2) lines(P2T3$TMP, col = "red", lwd = 2, lty = 2) #### Using the new way
par(mar = c(1, 5, 0, 0))  #set up the margins for the overall plot
quartz(height = 8, width = 8)
par(fig = c(0, 1, 0.65, 1), new = T)  #now tell it where you want the new plot, reads x1 x2, y1 y2 (left and right bounds, top and bottom bounds)

## Warning: calling par(new=TRUE) with no plot

par(mar = c(3, 6, 1, 1))  #set the margins for the new plot
plot.new()
plot(P2B1$TMP, ylab = "", xlab = "", type = "l", lty = 1, ylim = c(-25, 15), xaxt = "n", lwd = 3, las = 1, bty = "l", cex.axis = 1.5) mtext("3 January - 13 March, 2011", side = 1, line = 0.5, adj = 0.5, cex = 1.5) lines(P2T1$TMP, type = "l", lty = 4, col = "red", lwd = 2)
legend(x = 0, y = 19, legend = c("1m Height", "Ground Level"), col = c("red", "black"), lty = c(4,
1), lwd = c(3, 2), bty = "n")

par(fig = c(0, 1, 0.35, 0.7), new = T)
par(mar = c(3, 6, 1, 1))
plot.new()
plot(P2B2$TMP, ylab = (expression(paste("Temperature (", degree, "C)"))), xlab = "", type = "l", lty = 1, lwd = 3, ylim = c(-10, 35), xaxt = "n", bty = "l", las = 1, cex.axis = 1.5, cex.lab = 1.5) lines(P2T2$TMP, col = "red", lwd = 2, lty = 4)
mtext("13 March - 7 May, 2011", side = 1, line = 0.5, adj = 0.5, cex = 1.5)

par(fig = c(0, 1, 0, 0.35), new = T)
par(mar = c(3, 6, 1, 1))
plot.new()
plot(P2B3$TMP, ylab = "", xlab = "", type = "l", lty = 1, ylim = c(0, 38), xaxt = "n", lwd = 3, las = 1, bty = "l", cex.axis = 1.5) lines(P2T3$TMP, col = "red", lwd = 2, lty = 4)
mtext("7 May - 16 July, 2011", side = 1, line = 0.5, adj = 0.5, cex = 1.5) ############# Puting it all together
library(MASS)
library(MCMCpack)
library(compositions)
library(grDevices)

w <- rdirichlet(50000, c(5, 0.5, 2))
colnames(w) <- c("A", "B", "C")
ind1 <- rmultinom(1, 40, w[1, ])
ind2 <- rmultinom(1, 22, w[2, ])

quartz(width = 6.8, height = 4.5)
par(fig = c(0.4, 0.6, 0.75, 0.95), mar = c(0, 0, 0, 0))
plot.rcomp(w, col = rgb(1, 0, 0, 0.1), pch = ".", labels = c("A", "B", "C"))

# Individual count data
par(fig = c(0, 1, 0.1, 0.3), new = TRUE)
# plot.window(xlim=c(0,1),ylim=c(0,0.75))
plot.new()
# text(0.2,0.2,'x',font=3,family='Arial',cex=2)
text(0.1, 0.6, expression(italic(x[paste("1A")]) == 36), pos = 4)
text(0.1, 0.4, expression(italic(x[paste("1B")]) == 1), pos = 4)
text(0.1, 0.2, expression(italic(x[paste("1C")]) == 3), pos = 4)

text(0.4, 0.6, expression(italic(x[paste("2A")]) == 15), pos = 4)
text(0.4, 0.4, expression(italic(x[paste("2B")]) == 3), pos = 4)
text(0.4, 0.2, expression(italic(x[paste("2C")]) == 11), pos = 4)

text(0.74, 0.6, expression(italic(x[paste("iA")]) == 13), pos = 4)
text(0.74, 0.4, expression(italic(x[paste("iB")]) == 4), pos = 4)
text(0.74, 0.2, expression(italic(x[paste("iC")]) == 5), pos = 4)

# individual probs given count data
Px1 <- c(36, 1, 3)/40
Px2 <- c(15, 3, 11)/29
Px3 <- c(13, 4, 5)/22

par(fig = c(0.15, 0.25, 0.4, 0.6), new = TRUE)
plot.new()
barplot(Px1, names.arg = c(" "), ylim = c(0, 1), col = "red", cex.axis = 0.5, cex.names = 0.75,
las = 1)
mtext("A  B  C", side = 1)
abline(h = 0, lwd = 2)

par(fig = c(0.43, 0.53, 0.4, 0.6), new = TRUE)
plot.new()
barplot(Px2, names.arg = c(" "), ylim = c(0, 1), col = "red", cex.axis = 0.5, cex.names = 0.75,
las = 1)
mtext("A  B  C", side = 1)
abline(h = 0, lwd = 2)

par(fig = c(0.74, 0.84, 0.4, 0.6), new = TRUE)
# par(fig=c(0.71,0.81,0.4,0.6),new=TRUE)
plot.new()
barplot(Px3, names.arg = c(" "), ylim = c(0, 1), col = "red", cex.axis = 0.5, cex.names = 0.75,
las = 1)
mtext("A  B  C", side = 1)
abline(h = 0, lwd = 2)

par(fig = c(0, 1, 0, 1), new = TRUE)
plot.new()
text(0.62, 0.51, expression(...), pos = 2, cex = 2)
text(0.08, 0.5, expression(italic(Px[paste("1j", sep = "")]) == ""), pos = 2, cex = 1)
text(0.38, 0.5, expression(italic(Px[paste("2j", sep = "")]) == ""), pos = 2, cex = 1)
text(0.71, 0.5, expression(italic(Px[paste("ij", sep = "")]) == ""), pos = 2, cex = 1)
# text(0.68,0.5,expression(italic(Px[paste('ij',sep='')])==''),pos=2,cex=1)

text(0.04, 0.22, "Individual\ncounts", pos = 1, cex = 1)
text(-0.05, 0.65, "Individual probabilities", pos = 4, cex = 1)
text(0.04, 0.87, "Population", pos = 1, cex = 1)

arrows(0.16, 0.23, 0.16, 0.33, angle = 20, length = 0.15, lwd = 2)
arrows(0.46, 0.23, 0.46, 0.33, angle = 20, length = 0.15, lwd = 2)
arrows(0.795, 0.23, 0.795, 0.33, angle = 20, length = 0.15, lwd = 2)

arrows(0.53, 0.75, 0.7, 0.63, angle = 20, length = 0.15, lwd = 2, code = 3)
arrows(0.47, 0.75, 0.3, 0.63, angle = 20, length = 0.15, lwd = 2, code = 3)
arrows(0.5, 0.75, 0.5, 0.63, angle = 20, length = 0.15, lwd = 2, code = 3)

text(0.72, 0.89, expression(italic(alpha["A"]) == "5.0"), pos = 1, cex = 1)
text(0.72, 0.85, expression(italic(alpha["B"]) == "0.5"), pos = 1, cex = 1)
text(0.72, 0.81, expression(italic(alpha["C"]) == "2.0"), pos = 1, cex = 1)

text(0.92, 0.65, "Multinomial")
text(0.94, 0.87, "Dirichlet")

text(0.083, 0.95, expression(underline("Hierarchical level")), cex = 1.2)
text(0.89, 0.95, expression(underline("Modeled distribution")), cex = 1.2) 