etienne — Jun 6, 2013, 10:59 PM
# base graphics tutorial
# EXTRA MATERIAL
# Etienne Laliberte
# June 4, 2013
# tweaking plots
plot(pressure, type = "l", lwd = 3)
plot(pressure, type = "l", col= "red")
plot(pressure, type = "l", lty = "dashed")
plot(pressure, type = "l", ylim = c(0, 1200))
# customising graphics
# Type par() to list all values of parameters
# Some settings describe placement of plot
# Some settings describe aspects of device
# Some setting describe visual appearance
# par() has persistent effect
# calls within graphics function are temporary
# for all options, see
?par
starting httpd help server ...
done
# example of temporary effect within functions
# vs persistent effect of using par...
plot(pressure, col = "red")
par(col = "red")
plot(pressure) # points AND box are red because of par() effect!
plot(pressure, col = "blue") # points are blue!
# return to original colour
par(col = "black")
# adding text to a plot
plot(pressure, main = "Temperature-pressure relationship", las = 1,
xlab = expression(Temperature~(degree*C)),
ylab = "Pressure (mm Hg)")
eq <- expression(P == C~italic(e)^(-Delta*H[v] / RT ))
text(120, 700, eq)
# for info on math expressions, see
?plotmath
# arranging multiple plots per file
par(mfrow = c(2, 1) )
plot(pressure, type = "p")
mtext("a", adj = 0, line = 1, font = 2, cex = 1.5)
plot(pressure, type = "l")
mtext("b", adj = 0, line = 1, font = 2, cex = 1.5)
# arranging multiple plots per file: layout
# allows you to have plots of different sizes
layout(matrix(1:6, byrow = T, ncol = 2),
heights = c(2, 1, 1),
widths = c(1, 2))
layout.show(6)
for (i in 1:6) plot(pressure)
# get normal layout
layout(matrix(1) )
# 3D plots
head(volcano)
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 100 100 101 101 101 101 101 100 100 100 101 101 102
[2,] 101 101 102 102 102 102 102 101 101 101 102 102 103
[3,] 102 102 103 103 103 103 103 102 102 102 103 103 104
[4,] 103 103 104 104 104 104 104 103 103 103 103 104 104
[5,] 104 104 105 105 105 105 105 104 104 103 104 104 105
[6,] 105 105 105 106 106 106 106 105 105 104 104 105 105
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 102 102 102 103 104 103 102 101 101 102 103
[2,] 103 103 103 104 105 104 103 102 102 103 105
[3,] 104 104 104 105 106 105 104 104 105 106 107
[4,] 104 105 105 106 107 106 106 106 107 108 110
[5,] 105 105 106 107 108 108 108 109 110 112 114
[6,] 106 106 107 109 110 110 112 113 115 116 118
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 104 104 105 107 107 107 108 108 110 110 110
[2,] 106 106 107 109 110 110 110 110 111 112 113
[3,] 108 110 111 113 114 115 114 115 116 118 119
[4,] 111 114 117 118 117 119 120 121 122 124 125
[5,] 115 118 121 122 121 123 128 131 129 130 131
[6,] 119 121 124 126 126 129 134 137 137 136 136
[,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46]
[1,] 110 110 110 110 110 108 108 108 107 107 108
[2,] 114 116 115 114 112 110 110 110 109 108 109
[3,] 119 121 121 120 118 116 114 112 111 110 110
[4,] 126 127 127 126 124 122 120 117 116 113 111
[5,] 131 132 132 131 130 128 126 122 119 115 114
[6,] 135 136 136 136 135 133 129 126 122 118 116
[,47] [,48] [,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57]
[1,] 108 108 108 108 107 107 107 107 106 106 105
[2,] 109 109 109 108 108 108 108 107 107 106 106
[3,] 110 110 109 109 109 109 108 108 107 107 106
[4,] 110 110 110 109 109 109 109 108 108 107 107
[5,] 112 110 110 110 110 110 109 109 108 107 107
[6,] 115 113 111 110 110 110 110 109 108 108 108
[,58] [,59] [,60] [,61]
[1,] 105 104 104 103
[2,] 105 105 104 104
[3,] 106 105 105 104
[4,] 106 106 105 105
[5,] 107 106 106 105
[6,] 107 107 106 106
x <- 1:nrow(volcano)
y <- 1:ncol(volcano)
persp(x, y, volcano, theta = 135, phi = 30, shade = 0.75, col = "light blue")
contour(x, y, volcano)
image(x, y, volcano)
# scatterplot matrix
pairs(iris[, 1:4])
# a cooler version
# copy and paste these three functions
panel.hist <- function(x, ...)
{
usr <- par("usr"); on.exit(par(usr))
par(usr = c(usr[1:2], 0, 1.5) )
h <- hist(x, plot = FALSE)
breaks <- h$breaks; nB <- length(breaks)
y <- h$counts; y <- y/max(y)
rect(breaks[-nB], 0, breaks[-1], y, col="grey", ...)
}
panel.cor <- function(x, y, digits=2, prefix="", cex.cor, ...)
{
usr <- par("usr"); on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
r <- cor(x, y)
p.value <- cor.test(x, y)$p.value
is.sign <- p.value <= 0.05
txt <- format(c(r, 0.123456789), digits=digits)[1]
txt <- paste(prefix, txt, sep="")
if(missing(cex.cor)) cex.cor <- 0.8/strwidth(txt)
if (is.sign) text(0.5, 0.5, txt, cex = 1.2 * cex.cor, font = 2)
else text(0.5, 0.5, txt, cex = cex.cor, col = "grey50")
}
panel.smooth <- function (x, y, col = par("col"), bg = NA, pch = par("pch"),
cex = 1, col.smooth = "black", span = 2/3, iter = 3, ...)
{
p.value <- cor.test(x, y)$p.value
is.sign <- p.value <= 0.05
if (is.sign) points(x, y, pch = pch, col = "black", bg = bg, cex = cex)
else points(x, y, pch = pch, col = "grey50", bg = bg, cex = cex)
ok <- is.finite(x) & is.finite(y)
if (any(ok)) {
if (is.sign) lines(stats::lowess(x[ok], y[ok], f = span, iter = iter),
col = col.smooth, ...)
else lines(stats::lowess(x[ok], y[ok], f = span, iter = iter),
col = "grey50", ...)
}
}
# and now reate a new scatterplot matrix, way cooler!
pairs(iris[, 1:4], panel=panel.smooth, upper.panel = panel.cor, diag.panel = panel.hist)
