Visualisasi Data

Tujuan pembelajaran: memvisualisasikan data dengan fungsi-fungsi di R

Sumber: http://www.sthda.com

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R Base Graphs
Grafik-grafik Dasar R

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Fungsi-fungsi dasar R untuk membuat beberapa tipe plot

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Argumen-argumen untuk menyesuaikan plot

▪ pch: mengubah bentuk titik. Nilai yang diijinkan dari 1 sampai 25.
▪ cex: mengubah ukuran titik. Contoh: cex = 0.8.
▪ col: mengubah warna titik. Contoh: col = “blue”.
▪ frame: logical value. frame = FALSE removes the plot panel border frame.
▪ main, xlab, ylab. menentukan judul utama dan label sumbu x/y secara berturut-turut
▪ las: untuk teks sumbu x vertical gunakan las = 2.

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Data mtcars
▪ mtcars: Motor Trend Car Road Tests
▪ Sumber data: Henderson and Velleman (1981), Building multiple regression models
interactively. Biometrics, 37, 391–411.
▪ Deskripsi: data diekstraksi dari majalah Motor Trend AS 1974, dan terdiri dari konsumsi bahan bakar dan
10 aspek desain dan kinerja mobil dari 32 mobil (model 1973-74).
▪ Data terdiri dari 32 pengamatan dan 11 variabel:
[1] mpg Miles/(US) gallon
[2] cyl Number of cylinders
[3] disp Displacement (cu.in.)
[4] hp Gross horsepower
[5] drat Rear axle ratio
[6] wt Weight (1000 lbs)
[7] qsec 1/4 mile time
[8] vs Engine (0 = V-shaped, 1 = straight)
[9] am Transmission (0 = automatic, 1 = manual)
[10] gear Number of forward gears
[11] carb Number of carburetors
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Panggil data mtcars
> # panggil data mtcars
> data("mtcars")
> # struktur data mtcars
> str(mtcars)
'data.frame': 32 obs. of 11 variables:
$ mpg : num 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ...
$ cyl : num 6 6 4 6 8 6 8 4 4 6 ...
$ disp: num 160 160 108 258 360 ...
$ hp : num 110 110 93 110 175 105 245 62 95 123 ...
$ drat: num 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ...
$ wt : num 2.62 2.88 2.32 3.21 3.44 ...
$ qsec: num 16.5 17 18.6 19.4 17 ...
$ vs : num 0 0 1 1 0 1 0 1 1 1 ...
$ am : num 1 1 1 0 0 0 0 0 0 0 ...
$ gear: num 4 4 4 3 3 3 3 4 4 4 ...
$ carb: num 4 4 1 1 2 1 4 2 2 4 ...
> # Cetak 6 baris pertama
> head(mtcars, n=6)
mpg cyl disp hp drat wt qsec vs am gear carb
Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4
Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1
Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2
Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1

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Membuat plot dasar dengan fungsi plot()

> plot(x = mtcars$wt, y = mtcars$mpg,

pch = 16, frame = FALSE,
xlab = "wt", ylab = "mpg", col = "blue")

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Menyimpan plot dalam file pdf

> # Membuka file pdf

> pdf("C:/plot/rplot.pdf")
> # Membuat plot
> plot(x = mtcars$wt, y = mtcars$mpg,
pch = 16, frame = FALSE,
xlab = "wt", ylab = "mpg", col = "blue")
> # Menutup file pdf
> dev.off()

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Menyimpan plot dalam file jpeg

> # Membuka file jpeg

> jpeg("C:/plot/rplot.jpg", width = 350, height = 350)
> # Membuat plot
> plot(x = mtcars$wt, y = mtcars$mpg,
pch = 16, frame = FALSE,
xlab = "wt", ylab = "mpg", col = "blue")
> # Menutup file jpeg
> dev.off()

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Plot pencar dengan garis regresi linear sederhana

> plot(x = mtcars$wt, y = mtcars$mpg, main = "Plot pencar",

xlab = "wt", ylab = "mpg",
pch = 16, frame = FALSE,col="blue")
> abline(lm(mpg ~ wt, data = mtcars), col = "red", lwd =2)
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 Plot pencar dengan garis regresi menggunakan fungsi
scatterplot() dari paket car

> library(car)
> scatterplot(mpg ~ wt, data = mtcars,
smooth = FALSE, grid = FALSE, regLine=list(method=lm, lty=1, lwd=2, col="green"))
> scatterplot(mpg ~ wt, data = mtcars, xlab = "Weight",ylab="Miles per gallon",
smooth = FALSE, grid = FALSE, regLine=list(method=lm, lty=1, lwd=2, col="green"))

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Plot pencar dengan garis regresi berdasarkan grup (“cyl”)

> scatterplot(mpg ~ wt|cyl, data = mtcars, smooth = FALSE, grid = FALSE)

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 Plot pencar dengan label
pos a position specifier for the text. If specified this
overrides any adj value given. Values
of 1, 2, 3 and 4, respectively indicate positions
below, to the left of, above and to the right of the
specified (x,y) coordinates.

> scatterplot(mpg ~ wt, data = mtcars,regLine=FALSE,

smooth = FALSE, grid = FALSE, frame = FALSE)
> text(mtcars$wt, mtcars$mpg, labels=rownames(mtcars), cex= 0.7,pos=4,col="steelblue")

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Matriks plot pencar dengan fungsi pairs()

> pairs(mtcars)

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Matriks plot pencar untuk beberapa variabel
> pairs(mtcars[,c("mpg","disp","wt")], pch = 19)

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Boxplot
> #Boxplot untuk satu variabel
> boxplot(mtcars$mpg,ylab="mpg")
> #Boxplot berdasarkan grup (cyl) dengan frame
dihapus
> boxplot(mpg ~ cyl, data = mtcars, frame =
FALSE,xlab="cyt",ylab="mpg")
> #Boxplot horizontal
> boxplot(mpg ~ cyl, data = mtcars, frame =
FALSE, horizontal =
TRUE,xlab="cyt",ylab="mpg")
> #Boxplot dengan bentuk notch
> boxplot(mpg ~ cyl, data = mtcars, frame =
FALSE, notch = TRUE,xlab="cyt",ylab="mpg")

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> boxplot(mpg ~ cyl, data = mtcars, frame
= FALSE,border =
"steelblue",xlab="cyt",ylab="mpg")

> boxplot(mpg ~ cyl, data = mtcars, frame

= FALSE,border = c("#999999", "#E69F00",
"#56B4E9"),xlab="cyt",ylab="mpg")

> boxplot(mpg ~ cyl, data = mtcars, frame

= FALSE,col =
"steelblue",xlab="cyt",ylab="mpg")

> boxplot(mpg ~ cyl, data = mtcars, frame

= FALSE,col = c("#999999", "#E69F00",
"#56B4E9"),xlab="cyt",ylab="mpg")

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Box plot dengan beberapa grup
> boxplot(mpg ~ am*cyl, data = mtcars,
col = c("white", "steelblue"), frame = FALSE,xlab="am.cyl",ylab="mpg")

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Plot garis

> # mengurutkan data berdasarkan variabel wt (sumbu x)

> mtcars <- mtcars[order(mtcars$wt), ]
> plot(mtcars$wt, mtcars$mpg, type = "o", pch = 19,col = "steelblue", xlab = "wt", ylab = "mpg",
lwd=2,lty=2)

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 Plot untuk beberapa garis

> # mengurutkan data berdasarkan variabel wt (sumbu x)

> mtcars <- mtcars[order(mtcars$wt), ]
> # subset data berdasarkan cyl
> cyl4 <- subset(mtcars,cyl=="4")
> cyl6 <- subset(mtcars,cyl=="6")
> cyl8 <- subset(mtcars,cyl=="8")
> # membuat plot bingkai
> plot(mtcars$wt, mtcars$mpg, type = "o", pch = 19,col = "white", xlab = "wt", ylab = "mpg")
> # menambahkan beberapa garis
> lines(cyl4$wt, cyl4$mpg, pch = 18, col = "red", type = "o", lty = 1)
> lines(cyl6$wt, cyl6$mpg, pch = 18, col = "blue", type = "o", lty = 2)
> lines(cyl8$wt, cyl8$mpg, pch = 18, col = "green", type = "o", lty = 3)
> legend("topright", legend=c("cyl 4", "cyl 6","cyl 8"),col=c("red", "blue","green"), lty = c(1,2,3), cex=0.8,bty="n")

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Stripchart dengan fungsi stripchart()
▪ Fungsi stripchart():
stripchart(x, data = NULL method = "overplot", jitter = 0.1)
▪ Keterangan:
▪ x: the data from which the plots are to be produced. Allowed values are one or a
list of numeric vector, each corresponding to a component plot.
▪ data: a data.frame (or list) from which the variables in x should be taken.
▪ Method: the method to be used to separate coincident points. Allowed values are
one of “overplot”, “jitter” or “stack”.
▪ jitter: when method = “jitter” is used, jitter gives the amount of jittering applied.

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 Stripchart horisontal

> stripchart(mpg ~ cyl, data = mtcars,

pch = 19, frame = FALSE,xlab="mpg",ylab="cyl")

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Stripchart vertikal
>#plot vertical dengan metode jitter
> stripchart(mpg ~ cyl, data = mtcars,
pch = 19, frame = FALSE, vertical =
TRUE,method = "jitter",
xlab="cyl",ylab="mpg")

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 Stripchart dengan beda warna dan bentuk titik

> # Mengubah bentuk titik(pch) dan warna

berdasarkan grup
> stripchart(mpg ~ cyl, data = mtcars,
frame = FALSE, vertical = TRUE,
method = "jitter", pch = c(21, 18, 16),
col = c("#999999", "#E69F00", "#56B4E9"),
main = "mpg by cyle", xlab = "cyl", ylab
= "mpg")

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Plot bar dengan nilai frekuensi
> counts <- table(mtcars$gear)
> bp <- barplot(counts, main="Car Distribution",
xlab="Number of Gears", ylab ="Frequency",ylim=c(0,18))
> text(bp,counts+1, as.character(counts))

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Pie chart dari banyaknya mobil berdasarkan cyl
> mtcars$cyl <- factor(mtcars$cyl)
> counts <- table(mtcars$cyl)
> pie(counts, labels = levels(mtcars$cyl), radius = 1)

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Pie chart dengan frekuensi
> counts <- table(mtcars$cyl)
> labels <- c("cyl4", "cyl6", "cyl8")
> pct <- as.numeric(round(counts/sum(counts)*100))
> # menambahkan persen ke labels
> lbls <- paste(labels, pct)
> lbls <- paste(lbls,"%",sep="")
> pie(counts,labels = lbls, col=c("red","green","blue"),main="cylinder")

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Pie chart 3D

> library(plotrix)
> counts <- table(mtcars$cyl)
> labels <- c("cyl4", "cyl6", "cyl8")
> pct <- as.numeric(round(counts/sum(counts)*100))
> lbls <- paste(labels, pct)
> lbls <- paste(lbls,"%",sep="")
> pie3D(counts,labels = lbls, col=c("red","green","blue"))

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Pie chart 3D

> library(plotrix)
> counts <- table(mtcars$cyl)
> labels <- c("cyl4", "cyl6", "cyl8")
> pct <- as.numeric(round(counts/sum(counts)*100))
> lbls <- paste(labels, pct)
> lbls <- paste(lbls,"%",sep="")
> pie3D(counts,labels = lbls, col=c("red","green","blue"),explode=0.1)

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Histogram
▪ Histogram dapat dibuat dengan fungsi hist(). Aturan Sturges biasanya digunakan
untuk mendefinisikan titik-titik break antara sel-sel histogram
▪ Fungsi hist():
hist(x, breaks = "Sturges")
▪ Keterangan:
▪ x: a numeric vector
▪ breaks: breakpoints between histogram cells.

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Histogram dari mpg
> hist(mtcars$mpg,breaks="Sturges",xlab="mpg",main=NULL)

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Histogram
menentukan warna dan banyaknya break

> hist(mtcars$mpg, col = "violet",xlab="mpg",main=NULL,breaks = 10)

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Plot densitas bagi mpg
> # menghitung densitas data
> dens <- density(mtcars$mpg)
> # plot densitas
> plot(dens, frame = FALSE, col = "steelblue", main = "Density plot of mpg")

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Plot densitas
> plot(dens, frame = FALSE, col = "steelblue", main = "Density plot of mpg")
> # mengisi plot densitas
> polygon(dens, col = "steelblue")

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Dotchart
▪ Fungsi dotchart() digunakan untuk mengambar plot titik.
dotchart(x, labels = NULL, groups = NULL, gcolor = par("fg"),
color = par("fg"))
▪ Keterangan
▪ x: numeric vector or matrix
▪ labels: a vector of labels for each point.
▪ groups: a grouping variable indicating how the elements of x are grouped.
▪ gcolor: color to be used for group labels and values.
▪ color: the color(s) to be used for points and labels.

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Dotchart mpg

> mtcars <- mtcars[order(mtcars$mpg), ]

> dotchart(mtcars$mpg, labels = row.names(mtcars),cex = 0.6, xlab = "mpg")
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Dotchart mpg berdasarkan cylinder

> mtcars$cyl <- factor(mtcars$cyl)

> my_cols <- c("#999999", "#E69F00", "#56B4E9")
> dotchart(mtcars$mpg, labels = row.names(mtcars),groups = mtcars$cyl,gcolor = my_cols, color =
my_cols[mtcars$cyl],cex = 0.6, pch = 19, xlab = "mpg")

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Plot rata-rata grup
▪ Fungsi plotmeans() dalam paket gplot digunakan untuk memperoleh plot rata-rata
grup.
> plotmeans(mpg ~ cyl, data = mtcars, frame=FALSE)

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Plot rata-rata grup
▪ Menambahkan label rata-rata
(mean.labels = TRUE)
▪ Menghilangkan koneksi garis
(connect = FALSE)

> plotmeans(mpg ~ cyl, data = mtcars, frame = FALSE, mean.labels = TRUE, connect = FALSE)

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Paket Lattice

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Fungsi-fungsi dalam paket lattice

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Scatterplot dengan fungsi xyplot()

> library(lattice)
> xyplot(mpg ~ wt, data = mtcars)

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Scatterplot
menambahkan warna berdasarkan grup

> xyplot(mpg ~ wt,group = cyl,

data = mtcars, auto.key = TRUE)

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Scatterplot
menunjukkan titik-titik (“p”) grid (“g”) dan garis smoothing
mengubah nama sumbu x (xlab) dan sumbu y (ylab)

> xyplot(mpg ~ wt, data = mtcars,

type = c("p", "g", "smooth"),
xlab = "Weight (1000 lbs)", ylab = "Miles/(US) gallon")

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Multiple panels by group: y ~ x | group

> xyplot(mpg ~ wt | cyl,

group = cyl, data = mtcars,
type = c("p", "smooth"),
scales = "free")

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3D scatter plot dengan fungsi cloud()

> cloud(mpg ~ wt * hp, data = mtcars)

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3D scatterplot dengan warna berdasarkan grup

> cloud(mpg ~ wt * hp,

group = cyl, data = mtcars,
auto.key = TRUE)

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Basic plot: box plot, violin plot, dot plot, strip plot

> # box plot

> bwplot(mpg ~ cyl, data = mtcars,
xlab = "cyl", ylab = "mpg")

> # violin plot

> bwplot(mpg ~ cyl, data = mtcars,
panel = panel.violin,
xlab = "cyl", ylab = "mpg")

> # dot plot

> dotplot(mpg ~ cyl, data = mtcars,
xlab = "cyl", ylab = "mpg")

> # strip plot

> stripplot(mpg ~ cyl, data = mtcars,
jitter.data = TRUE, pch = 19,
xlab = "cyl", ylab = "mpg")

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Plot dengan beberapa grup
> mtcars$gear <- factor(mtcars$gear)
> # box plot
> bwplot(mpg ~ cyl | gear, data = mtcars,
layout = c(3, 1),
xlab = "cyl", ylab = "mpg")

> # violin plot

> bwplot(mpg ~ cyl | gear, data = mtcars,
layout = c(3, 1), panel = panel.violin,
xlab = "cyl", ylab = "mpg")

> # Dot plot

> dotplot(mpg ~ cyl | gear, data = mtcars,
layout = c(3, 1),
xlab = "cyl", ylab = "mpg")

> # Strip plot

> stripplot(mpg ~ cyl | gear, data = mtcars,
layout = c(3, 1), jitter.data = TRUE,
xlab = "cyl", ylab = "mpg")

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Plot densitas dan histogram

> # plot densitas

> densityplot(~ mpg, data =mtcars,
plot.points = FALSE)

> # histogram
➢ histogram(~ mpg, data =mtcars,
➢ breaks = "Sturges")

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Plot densitas berdasarkan grup
> densityplot(~ mpg, groups = cyl, data = mtcars,
plot.points = FALSE, auto.key =TRUE)

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Paket ggplot2
Box plot, violin plot, dot plot, stripchart, density plot, histogram plot,
scatter plot, bar plot, line plot, pie chart, Q-Q plot

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ggplot2
▪ ggplot2 adalah paket R yang sangat berguna dan fleksibel untuk memproduksi
grafik-grafik yang elegan. Paket ini diimplementasikan oleh Hadley Wickham.
▪ Konsep dari ggplot2 adalah membagi plot dalam tiga bagian fundamental
berbeda: Plot = data + Aesthetics + Geometry.
▪ Komponen-kompen prinsip dari setiap plot dapat didefinisikan sebagai berikut:
▪ data adalah data frame
▪ Aesthetics digunakan untuk mengidentifikasikan variabel x dan y. Komponen ini
juga dapat untuk mengontrol warna, ukuran, dan bentuk titik-titik, panjang bar,
dll.
▪ Geometry mendefinisikan tipe grafik (histogram, box plot, line plot, density
plot, dot plot, ….)
▪ Ada dua fungsi utama dalam paket ggplot2 yaitu: fungsi qplot() dan ggplot().
▪ qplot() berarti quick plot, digunakan untuk memproduksi plot sederhana secara
mudah
▪ ggplot() lebih fleksibel dan luas penggunaannya daripada qplot yang membangun
plot secara bertahap.

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Fungsi qplot()
▪ Fungsi qplot() adalah
qplot(x, y=NULL, data, geom="auto", xlim = c(NA, NA), ylim =c(NA, NA))
▪ Keterangan:
▪ x : x values
▪ y : y values (optional)
▪ data : data frame to use (optional).
▪ geom : Character vector specifying geom to use. Defaults to “point” if x and y are
specified, and “histogram” if only x is specified.
▪ xlim, ylim: x and y axis limits
▪ main: Plot title
▪ xlab, ylab: x and y axis labels

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Plot pencar dasar
> library(ggplot2)
> # plot pencar
> qplot(x = wt,y = mpg, data = mtcars)
> # menambahkan garis
> qplot(x = wt, y = mpg, data = mtcars, geom=c("point", "line"))

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Plot pencar dengan garis yang diperhalus (smoothed line)
> # garis yang diperhalus
> qplot(wt, mpg, data = mtcars, geom = c("point", "smooth"))
> # garis yang diperhalus berdasarkan grup
> qplot(wt, mpg, data = mtcars, color = factor(cyl),geom=c("point", "smooth"))

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Plot pencar
mengubah warna pada plot pencar

> qplot(wt,mpg, data = mtcars, colour = cyl)

> # menambahkan garis
> qplot(wt,mpg, data = mtcars, colour = cyl, geom=c("point", "line"))
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Plot pencar
mengubah bentuk dan ukuran titik-titik

> qplot(wt,mpg, data = mtcars, shape = cyl)

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Plot pencar dengan teks

> qplot(wt,mpg, data = mtcars, label = rownames(mtcars),

geom=c("point", "text"),
hjust=0, vjust=0)
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Box plot, dot plot, & violin plot

> # box plot

> qplot(cyl, mpg, data = mtcars, geom=c("boxplot"))
> # dot plot
> qplot(cyl, mpg, data = mtcars, geom=c("dotplot"), stackdir = "center", binaxis = "y")
> # violin plot
> qplot(cyl, mpg, data = mtcars, geom=c("violin"), trim = FALSE)

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Box plot, dot plot, & violin plot

> # box plot

> qplot(cyl, mpg, data = mtcars, geom = c("boxplot", "jitter"), fill = cyl)
> # dot plot
> qplot(cyl, mpg, data = mtcars, geom = "dotplot", stackdir = "center", binaxis = "y", color = cyl, fill = cyl)
> # violin plot
> qplot(cyl, mpg, data = mtcars, geom = c("violin"), trim = FALSE, fill = cyl)

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Histogram plot

> # histogram dasar

> qplot(mpg, data = mtcars, geom = "histogram")
> # menambahkan warna berdasarkan cyl
> qplot(mpg, data = mtcars, geom = "histogram", fill = cyl)

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Density plot

> # plot densitas dasar

> qplot(mpg, data = mtcars, ylab = "Density" ,geom = "density")
> # menambahkan garis warna berdasarkan grup cyl
> qplot(mpg, data = mtcars,ylab = "Density", geom = "density",
color = cyl, linetype = cyl)

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ggplot2: box plot
▪ Fungsi geom_boxplot() digunakan untuk membuat suatu plot kotak.
geom_boxplot(outlier.colour="black", outlier.shape=16,
outlier.size=2, notch=FALSE)
▪ Keterangan:
▪ outlier.colour, outlier.shape, outlier.size : The color, the shape and the size for
outlying points
▪ notch : logical value. If TRUE, make a notched box plot. The notch displays a
confidence interval around the median which is normally based on the median +/-
1.58*IQR/sqrt(n). Notches are used to compare groups; if the notches of two
boxes do not overlap, this is a strong evidence that the medians differ.

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Box plot
> library(ggplot2)
> # box plot dasar
> p <- ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_boxplot()
> p
> # merotasi box plot
> p + coord_flip()

> # notched box plot

> ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_boxplot(notch=TRUE)

> # mengubah outlier, warna, bentuk, dan ukuran

> ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_boxplot(outlier.colour="red",
outlier.shape=8,outlier.size=4)

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Box plot

> # Box plot dengan titik rata-rata

> p + stat_summary(fun.y=mean, geom="point", shape=23, size=4)
> # Box plot dengan dot plot
> p + geom_dotplot(binaxis='y', stackdir='center', dotsize=1)
> # Box plot dengan titik jitter
> p + geom_jitter(shape=16, position=position_jitter(0.2))

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Box plot
mengubah garis box plot berdasarkan grup
Mengubah secara manual warna garis box plot
menggunakan fungsi:
▪ scale_color_manual() : to use custom colors
▪ scale_color_brewer() : to use color palettes
from RColorBrewer package
▪ scale_color_grey() : to use grey color palettes

> # menambahkan warna garis boxplot berdasarkan grup

> p<-ggplot(mtcars, aes(x=cyl, y=mpg, color=cyl)) +
geom_boxplot()
> p
> # menggunakan custom color palletes
> p+scale_color_manual(values=c("#999999", "#E69F00",
"#56B4E9"))
> # menggunakan brewer color palletes
> p+scale_color_brewer(palette="Dark2")
> # menggunakan warna abu-abu
> p + scale_color_grey() + theme_classic()

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Box plot
menggubah warna dalam box plot

> p<-ggplot(mtcars, aes(x=cyl, y=mpg, fill=cyl)) +

geom_boxplot()
> p
> p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
> p+scale_fill_brewer(palette="Dark2")
> p + scale_fill_grey() + theme_classic()

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Box plot
mengubah posisi legend

> p + theme(legend.position="top")
> p + theme(legend.position="bottom")
> p + theme(legend.position="none") # menghapus legend

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Box plot dengan beberapa grup

> mtcars$am <- factor(mtcars$am)

> ggplot(mtcars, aes(x=cyl, y=mpg, fill=am)) +
geom_boxplot()

> # mengubah posisi

> p<-ggplot(mtcars, aes(x=cyl, y=mpg, fill=am)) +
geom_boxplot(position=position_dodge(1))
> p
> # menambahkan dot
> p + geom_dotplot(binaxis='y', stackdir='center’,
position=position_dodge(1))
> # mengubah warna
> p+scale_fill_manual(values=c("#999999", "#E69F00",
"#56B4E9"))

70
Violin plot

> library(ggplot2)
> # Basic violin plot
> p <- ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_violin()
> p
> # rotate the violin plot
> p + coord_flip()
> # Set trim argument to FALSE
> ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_violin(trim=FALSE)

71
Violin plot
menambahkan titik rata-rata dan median

# violin plot with mean points

p + stat_summary(fun.y=mean, geom="point", shape=23, size=2)
# violin plot with median points
p + stat_summary(fun.y=median, geom="point", size=2, color="red")

72
Violin plot
menambahkan median dan kuartil

p + geom_boxplot(width=0.1)

73
Violin plot
menambahkan rata-rata dan simpangan baku

▪ The function mean_sdl is

used. mean_sdl computes
the mean plus or minus
a constant times the standard
deviation.
▪ In the R code below, the constant
is specified using the
argument mult (mult = 1). By
default mult = 2.
▪ The mean +/- SD can be added
as a crossbar or a pointrange.

> p <- ggplot(mtcars, aes(x=cyl, y=mpg)) +

geom_violin(trim=FALSE)
> library(Hmisc)
> p + stat_summary(fun.data="mean_sdl", mult=1,
geom="crossbar", width=0.2 )
> p + stat_summary(fun.data=mean_sdl, mult=1,
geom="pointrange", color="red")
74
Violin plot
menambahkan formula statistik ringkasan

# Function to produce summary statistics

(mean and +/- sd)
data_summary <- function(x) {
m <- mean(x)
ymin <- m-sd(x)
ymax <- m+sd(x)
return(c(y=m,ymin=ymin,ymax=ymax))
}
p + stat_summary(fun.data=data_summary)

75
Violin plot with dots

# violin plot with dot plot

p + geom_dotplot(binaxis='y', stackdir='center', dotsize=1)
# violin plot with jittered points # 0.2 : degree of jitter in x direction
p + geom_jitter(shape=16, position=position_jitter(0.2))

76
Violin plot colors by groups

# Change violin plot line colors by groups

p<-ggplot(mtcars, aes(x=cyl, y=mpg, color=cyl)) +
geom_violin(trim=FALSE)
P
# Use custom color palettes
p+scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# Use brewer color palettes
p+scale_color_brewer(palette="Dark2")
# Use grey scale
p + scale_color_grey() + theme_classic()

77
Violin plot fill colors

p<-ggplot(mtcars, aes(x=cyl, y=mpg, fill=cyl)) +

geom_violin(trim=FALSE)
p
# Use custom color palettes
p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# Use brewer color palettes
p+scale_fill_brewer(palette="Dark2")
# Use grey scale
p + scale_fill_grey() + theme_classic()

78
Violin plot with multiple groups

> ggplot(mtcars, aes(x=cyl, y=mpg, fill=am)) +

geom_violin()
> p + geom_dotplot(binaxis='y', stackdir='center’,
position=position_dodge(1))
> p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))

79
Dot plot

# dotplot
library(ggplot2)
# Basic dot plot
p<-ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_dotplot(binaxis='y', stackdir='center')
p
# Change dotsize and stack ratio
ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_dotplot(binaxis='y', stackdir='center',
stackratio=1.5, dotsize=1.2)
# Rotate the dot plot
p + coord_flip()
80
Dot plot
Add mean and median points

# dot plot with mean points

p + stat_summary(fun.y=mean, geom="point", shape=18, size=3, color="red")
# dot plot with median points
p + stat_summary(fun.y=median, geom="point", shape=18, size=3, color="red")

81
Dot plot with box plot and violin plot

# Add basic box plot

ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_boxplot()+
geom_dotplot(binaxis='y', stackdir='center')
# Add notched box plot
ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_boxplot(notch = TRUE)+
geom_dotplot(binaxis='y', stackdir='center')
# Add violin plot
ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_violin(trim = FALSE)+
geom_dotplot(binaxis='y', stackdir='center')

82
Dot plot colors by groups

# Use single fill color

ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_dotplot(binaxis='y', stackdir='center', fill="#FFAAD4")
# Change dot plot colors by groups
p<-ggplot(mtcars, aes(x=cyl, y=mpg, fill=cyl)) +
geom_dotplot(binaxis='y', stackdir='center')
p

83
# Use custom color palettes
p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# Use brewer color palettes
p+scale_fill_brewer(palette="Dark2")
# Use grey scale
p + scale_fill_grey() + theme_classic()

84
Dot plot
Change the legend position

p + theme(legend.position="top")
p + theme(legend.position="bottom")
p + theme(legend.position="none") # Remove legend

85
Dot plot with multiple groups

> ggplot(mtcars, aes(x=cyl, y=mpg, fill=am)) +

geom_dotplot(binaxis='y', stackdir='center')

> p<-ggplot(mtcars, aes(x=cyl, y=mpg, fill=am)) +

geom_dotplot(binaxis='y', stackdir='center',
position=position_dodge(0.8))
> p

86
Customized dot plots

# Basic dot plot

ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_boxplot()+
geom_dotplot(binaxis='y', stackdir='center')+
labs(title="Plot of mpg by cyl",x="cyl", y = "mpg")+
theme_classic()
# Change color by groups
dp <-ggplot(mtcars, aes(x=cyl, y=mpg, fill=cyl)) +
geom_dotplot(binaxis='y', stackdir='center')+
labs(title="Plot of mpg by cyl",x="cyl", y = "mpg")
dp + theme_classic()
87
ggplot2: stripchart()

library(ggplot2)
# Basic stripchart
ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_jitter()
# Change the position # 0.2 : degree of jitter in x direction
p<-ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_jitter(position=position_jitter(0.2))
p
# Rotate the stripchart
p + coord_flip()

88
Stripchart
Change point shapes and size

# Change point size

ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_jitter(position=position_jitter(0.2), cex=1.2)
# Change shape
ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_jitter(position=position_jitter(0.2), shape=17)

89
Stripchart
Add mean and median points

# stripchart with mean points

p + stat_summary(fun.y=mean, geom="point", shape=18, size=3, color="red")
# stripchart with median points
p + stat_summary(fun.y=median, geom="point", shape=18, size=3, color="red")

90
 Stripchart with box blot and violin plot

# Add basic box plot

ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_boxplot()+
geom_jitter(position=position_jitter(0.2))
# Add notched box plot
ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_boxplot(notch = TRUE)+
geom_jitter(position=position_jitter(0.2))
# Add violin plot
ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_violin(trim = FALSE)+
geom_jitter(position=position_jitter(0.2))

91
 Stripchart
colors by groups

mtcars$am <- factor(mtcars$am)

p<-ggplot(mtcars, aes(x=cyl, y=mpg, color=am)) +
geom_jitter(position=position_jitter(0.2))
p
# Use custom color palettes
p+scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# Use brewer color palettes
p+scale_color_brewer(palette="Dark2")
# Use grey scale
p + scale_color_grey() + theme_classic()

92
Stripchart
change the legend position

p + theme(legend.position="top")
p + theme(legend.position="bottom")
p + theme(legend.position="none")# Remove legend

93
 Stripchart
Change stripchart colors and add box plots

> p+scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))

> mtcars$am <- factor(mtcars$am)
> mtcars$cyl <- factor(mtcars$cyl)
> ggplot(mtcars, aes(x=cyl, y=mpg, color=am)) +
geom_boxplot(color="black")+
geom_jitter(position=position_jitter(0.2))
> ggplot(mtcars, aes(x=cyl, y=mpg, color=am)) +
geom_boxplot(position=position_dodge(0.8))+
geom_jitter(position=position_dodge(0.8))

94
Stripchart
customized

# Basic stripchart
ggplot(mtcars, aes(x=cyl, y=mpg)) +
geom_boxplot()+
geom_jitter(position=position_jitter(0.2))+
labs(title="Plot of mpg by cyl",x="cyl", y = "mpg")+
theme_classic()
# Change color/shape by groups
p <- ggplot(mtcars, aes(x=cyl, y=mpg, color=cyl, shape=cyl)) +
geom_jitter(position=position_jitter(0.2))+
labs(title="Plot of mpg by cyl",x="cyl", y = "mpg")
p + theme_classic()

95
Density plots: basic

library(ggplot2)
# Basic density
p <- ggplot(mtcars, aes(x=mpg)) +
geom_density()
p
# Add mean line
p+ geom_vline(aes(xintercept=mean(mpg)),
color="blue", linetype="dashed", size=1)

96
Density plot line types and colors

> # Change line color and fill color

> ggplot(mtcars, aes(x=mpg))+
geom_density(color="darkblue", fill="lightblue")
> # Change line type
> ggplot(mtcars, aes(x=mpg))+
geom_density(linetype="dashed")
97
Density plot colors by groups

# Change density plot line colors by groups

ggplot(mtcars, aes(x=mpg, color=cyl)) +
geom_density()

# Calculate mu for each grup

library(plyr)
mu <- ddply(mtcars, "cyl", summarise, grp.mean=mean(mpg))
head(mu)

# Add mean lines

p<-ggplot(mtcars, aes(x=mpg, color=cyl)) +
geom_density()+
geom_vline(data=mu, aes(xintercept=grp.mean, color=cyl),
linetype="dashed")
p

98
# Use custom color palettes
p+scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# Use brewer color palettes
p+scale_color_brewer(palette="Dark2")
# Use grey scale
p + scale_color_grey() + theme_classic()

99
 Density plot
Change fill colors

# Change density plot fill colors by groups

ggplot(mtcars, aes(x=mpg, fill=cyl)) +
geom_density()
# Use semi-transparent fill
p<-ggplot(mtcars, aes(x=mpg, fill=cyl)) +
geom_density(alpha=0.4)
p
# Add mean lines
p+geom_vline(data=mu, aes(xintercept=grp.mean, color=cyl),
linetype="dashed")
100
# Use custom color palettes
p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# use brewer color palettes
p+scale_fill_brewer(palette="Dark2")
# Use grey scale
p + scale_fill_grey() + theme_classic()

101
Density plot
Change the legend position

p + theme(legend.position="top")
p + theme(legend.position="bottom")
p + theme(legend.position="none") # Remove legend

102
Combine histogram and density plots

# Histogram with density plot

ggplot(mtcars, aes(x=mpg)) +
geom_histogram(aes(y=..density..), colour="black", fill="white")+
geom_density(alpha=.2, fill="#FF6666")
# Color by groups
ggplot(mtcars, aes(x=mpg, color=cyl, fill=cyl)) +
geom_histogram(aes(y=..density..), alpha=0.5,
position="identity")+
geom_density(alpha=.2)
103
 Density function
Use facets

p<-ggplot(mtcars, aes(x=mpg))+
geom_density()+facet_grid(cyl ~ .)
p
# Add mean lines
p+geom_vline(data=mu, aes(xintercept=grp.mean, color="red"),
linetype="dashed")

104
 Customized density plots

# Basic density
ggplot(mtcars, aes(x=mpg, fill=cyl)) +
geom_density(fill="gray")+
geom_vline(aes(xintercept=mean(mpg)), color="blue",
linetype="dashed")+
labs(title="mpg density curve",x="mpg", y = "density")+
theme_classic()
# Change line colors by groups
p<- ggplot(mtcars, aes(x=mpg, color=cyl)) +
geom_density()+
geom_vline(data=mu, aes(xintercept=grp.mean, color=cyl),
linetype="dashed")+
labs(title="mpg density curve",x="mpg", y = "density")
p

105
Scatter plot: basic

library(ggplot2)
# Basic scatter plot
ggplot(mtcars, aes(x=wt, y=mpg)) + geom_point()
# Change the point size, and shape
ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point(size=2, shape=23)

106
# Change the point size
mtcars$gear <- factor(mtcars$gear)
ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point(aes(size=gear))
# With text
ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point() +
geom_text(label=rownames(mtcars))

107
Scatter plot
Add regression lines

# Add the regression line

ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point()+
geom_smooth(method=lm)
# Remove the confidence interval
ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point()+
geom_smooth(method=lm, se=FALSE)
# Loess method
ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point()+
geom_smooth()

108
Scatter plot
Change the appearance of points and lines

# Change the point colors and shapes

# Change the line type and color
ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point(shape=18, color="blue")+
geom_smooth(method=lm, se=FALSE, linetype="dashed", color="darkred")
# Change the confidence interval fill color
ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point(shape=18, color="blue")+
geom_smooth(method=lm, linetype="dashed", color="darkred", fill="blue")

109
Scatter plots with multiple groups
Change the point color/shape/size automatically

# Change point shapes by the levels of cyl

ggplot(mtcars, aes(x=wt, y=mpg, shape=cyl)) +
geom_point()
# Change point shapes and colors
ggplot(mtcars, aes(x=wt, y=mpg, shape=cyl, color=cyl)) +
geom_point()
# Change point shapes, colors and sizes
ggplot(mtcars, aes(x=wt, y=mpg, shape=cyl, color=cyl, size=cyl)) +
geom_point()
110
 Customized scatter plots

# Basic scatter plot

ggplot(mtcars, aes(x=wt, y=mpg)) +
geom_point()+
geom_smooth(method=lm, color="black")+
labs(title="Miles per gallon \n according to the weight",
x="Weight (lb/1000)", y = "Miles/(US) gallon")+
theme_classic()
# Change color/shape by groups
# Remove confidence bands
p <- ggplot(mtcars, aes(x=wt, y=mpg, color=cyl, shape=cyl)) +
geom_point()+
geom_smooth(method=lm, se=FALSE, fullrange=TRUE)+
labs(title="Miles per gallon \n according to the weight",
x="Weight (lb/1000)", y = "Miles/(US) gallon")
p + theme_classic()

111
Bar plot

# Barplot
library(ggplot2)
# Basic barplot
p<-ggplot(data=mtcars, aes(x=cyl, y=mpg)) +
geom_bar(stat="identity")
p

# Horizontal bar plot

p + coord_flip()

112
Bar plot
change barplot fill colors by groups

# Change barplot fill colors by groups

p<-ggplot(mtcars, aes(x=cyl, y=mpg, fill=cyl)) +
geom_bar(stat="identity")+theme_minimal()
p
# Use custom color palettes
p+scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# use brewer color palettes
p+scale_fill_brewer(palette="Dark2")
# Use grey scale
p + scale_fill_grey()

113
Bar plot with multiple groups

# Stacked barplot with multiple groups

ggplot(data=mtcars, aes(x=cyl, y=mpg, fill=am)) +
geom_bar(stat="identity")
# Use position=position_dodge()
ggplot(data=mtcars, aes(x=cyl, y=mpg, fill=am)) +
geom_bar(stat="identity",
position=position_dodge())

114
Pie chart

# pie chart
library(ggplot2)
# Barplot
bp<- ggplot(mtcars, aes(x="", y=mpg, fill=cyl))+
geom_bar(width = 1, stat = "identity")
bp
pie <- bp + coord_polar("y", start=0)
pie

115
Pie chart
Change the pie chart fill colors

# Use custom color palettes

pie + scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# use brewer color palettes
pie + scale_fill_brewer(palette="Dark2")
pie + scale_fill_brewer(palette="Blues")+
theme_minimal()
# Use grey scale
pie + scale_fill_grey() + theme_minimal()
116
Basic histogram plots

library(ggplot2)
# Basic histogram
ggplot(mtcars, aes(x=mpg)) + geom_histogram()
# Change the width of bins
ggplot(mtcars, aes(x=mpg)) +
geom_histogram(binwidth=1)
# Change colors
p<-ggplot(mtcars, aes(x=mpg)) +
geom_histogram(color="black", fill="white")
p

117
Histogram with density plot

ggplot(mtcars, aes(x=mpg)) +
geom_histogram(aes(y=..density..),
colour="black", fill="white")+
geom_density(alpha=.2, fill="#FF6666")

118
Histogram plot colors by groups

# Change histogram plot line colors by groups

ggplot(mtcars, aes(x=mpg, color=cyl, fill = cyl)) +
geom_histogram(position="identity")
# Overlaid histograms
ggplot(mtcars, aes(x=mpg, color=cyl, fill = cyl)) +
geom_histogram(alpha=0.5, position="identity")

119
 Customized histogram plots

ggplot(mtcars, aes(x=mpg, color=cyl, fill=cyl)) +

geom_histogram(position="identity", alpha=0.5)+
geom_vline(data=mu, aes(xintercept=grp.mean,
color=cyl), linetype="dashed")+
scale_color_manual(values=c("#999999", "#E69F00",
"#56B4E9"))+
scale_fill_manual(values=c("#999999", "#E69F00",
"#56B4E9"))+
labs(title="mpg histogram plot",x="mpg", y =
"count")+
theme_classic()

120
Line plot

library(ggplot2)
# Basic line plot with points
ggplot(data=df, aes(x=cyl, y=grp.mean, group=1)) +
geom_line()+
geom_point()+
labs(x = "cyl", y = "mpg")
# Change the line type
ggplot(data=df, aes(x=cyl, y=grp.mean, group=1)) +
geom_line(linetype ="dashed")+
geom_point()+
labs(x = "cyl", y = "mpg")

121
Line plot with multiple groups
> library(plyr)
> df2 <- ddply(mtcars, c("cyl","am"), summarise, grp.mean=mean(mpg))
> df2 <- df2[order(df2$am), ]
> head(df2)
cyl am grp.mean
1 4 0 22.90000
3 6 0 19.12500
5 8 0 15.05000
2 4 1 28.07500
4 6 1 20.56667
6 8 1 15.40000
> ggplot(df2, aes(x=cyl, y=grp.mean, group=am)) +
geom_line(aes(linetype=am, color=am))+
geom_point(aes(color=am))+
theme(legend.position="top")+
labs(x = "cyl", y = "mpg")

122