04/22/2025

HORT 299/399 Special Seminar

An Introduction to
Data Analysis &
Visualization Using R

• a brief introduction to R and R Studio

• focus on R packages:
• ggplot2
• agricolae
• for each package, we will cover:
• short background
• general syntax
• commonly-used functions with examples (using built-in R datasets)

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• programming language widely used for statistical computing

and analysis
• supports data manipulation, calculation, and graphical display
• developed by Ross Ihaka and Robert Gentleman at the
University of Auckland, New Zealand
• open-source and free
• cross-platform compatible
• highly-extensible

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• multi-functional open-source IDE (integrated development

environment)
• graphical front-end to R (version 3.0.1 or higher)
• adapted to other programming languages (Python or SQL)
• features:
• auto-completes code
• versatile and customizable
• writing and saving reusable scripts
• operational history tracking
• exhaustive help on any subject

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Assignment Operator
# uses '<-' symbol to assign values to objects
x <- 5

Comments
# anything following '#' on a line is ignored by R
# allows you to include explanatory notes in your code

Vectors
vector <- c(1, 2, 3)

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Data frame
df <- data.frame(Name=c("Jhoana", "Pablo"), Score=c(90, 85))

Commands and Functions

mean(df$Score)
## [1] 87.5

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Package Installation
# install the 'ggplot2' package
install.packages("ggplot2")
install.packages("agricolae")

Package Loading
# load the 'ggplot2' package
library(ggplot2)
library(agricolae)

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Built-in Datasets
library(agricolae) # load the package containing the built-in
dataset
data(yacon) # load built-in datasets
head(yacon, 3) # displays first 3 rows of the dataset

## locality site dose entry replication height stalks wfr wff wfk roots FOS
## 1 CAJ 1 F0 P1385 1 57.9 3.2 6700 3600 5490 21.9 60.2
## 2 CAJ 1 F0 P1385 2 62.1 3.0 6450 2500 3800 21.3 60.4
## 3 CAJ 1 F0 P1385 3 53.7 2.6 7550 2450 5360 21.8 54.5
## glucose fructose sucrose brix foliage dry IH
## 1 1.74 5.0 26.66 14.8 25.6 15.6 0.3469
## 2 1.50 4.5 28.84 15.7 27.2 17.0 0.3257
## 3 2.14 9.3 27.06 14.3 30.0 15.9 0.3221

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Base R
# imports a csv file using a built-in function from baseR
data_csv <- read.csv("path/to/your/data.csv")
head(data_csv)

R Package
# imports an Excel file using 'readxl' package
install.packages("readxl")
library(readxl)

data_excel <- read_excel("path/to/your/data.csv")

head(data_excel)

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ggplot2

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ggplot2
• data visualization package built on the grammar of graphics
• creates complex and multi-layered graphics easily
General Syntax
ggplot(data, aes(x, y)) +
geom_<type>() +
theme_<style>() +
labs(title, x, y)

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ggplot2

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ggplot2 iris

Create the Base Plot

# create the base boxplot plot
ggplot(iris, aes(x = Species,
y = Sepal.Length)) +
geom_boxplot()

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ggplot2 iris

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ggplot2 iris
ggplot(iris, aes(x = Species,
y = Sepal.Length,
fill = Species)) + #
boxplot colors accdng to Species
geom_boxplot() +
labs(title = "Sepal Length by
Species",
x = "Species",
y = "Sepal Length (cm)") # add
labels

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ggplot2 iris
ggplot(iris, aes(x = Species,
y = Sepal.Length,
fill = Species)) + #
boxplot colors accdng to Species
geom_boxplot() +
labs(title = "Sepal Length by
Species",
x = "Species",
y = "Sepal Length (cm)") # add
labels

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ggplot2 iris
ggplot(iris, aes(x = Species,
y = Sepal.Length,
fill = Species)) + #
boxplot colors accdng to Species
geom_boxplot(width = 0.5) + # modify
box width
labs(title = "Sepal Length by
Species",
x = "Species",
y = "Sepal Length (cm)") # add
labels

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ggplot2 iris
ggplot(iris, aes(x = Species,
y = Sepal.Length,
fill = Species)) + #
boxplot colors accdng to Species
geom_boxplot(width = 0.5) + # modify
box width
labs(title = "Sepal Length by
Species",
x = "Species",
y = "Sepal Length (cm)") + #add
labels
geom_jitter() # add data points

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ggplot2 iris
ggplot(iris, aes(x = Species,
y = Sepal.Length,
fill = Species)) + #
boxplot colors accdng to Species
geom_boxplot(width = 0.5) + # modify
box width
labs(title = "Sepal Length by
Species",
x = "Species",
y = "Sepal Length (cm)") + # add
labels
geom_jitter(alpha = 0.25) # add data
points, modify transparency

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ggplot2

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ggplot2 Soybean

Create the Base Plot

# create the base line graph
ggplot(soybean, aes(x = Time,
y = weight)) +
geom_line()

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ggplot2 Soybean

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ggplot2 Soybean
ggplot(soybean, aes(x = Time,
y = weight,
color = Variety)) +
# add lines with different colors for
each variety
geom_line() +
labs(title = "Average Leaf Weight Over
Time",
x = "Days after planting (DAP)",
y = "Average Leaf Weight (g)") #
add labels

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ggplot2 Soybean
ggplot(soybean, aes(x = Time,
y = weight,
color = Variety)) +
# add lines with different colors for
each variety
geom_point() + # add data points
geom_line() +
labs(title = "Average Leaf Weight Over
Time",
x = "Days after planting (DAP)",
y = "Average Leaf Weight (g)") #
add labels

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ggplot2 Soybean
ggplot(soybean, aes(x = Time,
y = weight,
color = Variety)) +
# add lines with different colors for
each variety
geom_point(shape=18, size=3) + # add
data points, modify points
geom_line() +
labs(title = "Average Leaf Weight Over
Time",
x = "Days after planting (DAP)",
y = "Average Leaf Weight (g)") #
add labels

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ggplot2 Soybean
ggplot(soybean, aes(x = Time,
y = weight,
color = Variety)) +
# add lines with different colors for
each variety
geom_point(shape=18, size=3) + # add
data points, modify points
geom_line(linewidth=1.2) + # make
lines thicker
labs(title = "Average Leaf Weight Over
Time",
x = "Days after planting (DAP)",
y = "Average Leaf Weight (g)") #
add labels

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ggplot2 Soybean
ggplot(soybean, aes(x = Time,
y = weight,
linetype = Variety))
+ # add lines with different linetypes
for each variety
geom_point(shape=18, size=3) + # add
data points, modify points
geom_line(linewidth=1.2) + # make
lines thicker
labs(title = "Average Leaf Weight Over
Time",
x = "Days after planting (DAP)",
y = "Average Leaf Weight (g)") #
add labels

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ggplot2 Soybean
ggplot(soybean, aes(x = Time,
y = weight,
linetype = Variety))
+ # add lines with different linetypes
for each variety
geom_point(shape=18, size=3) + # add
data points, modify points
geom_line(linewidth=1.2) + # make
lines thicker
scale_linetype_manual(values =
c("dotdash", "solid")) + # specify line
types
labs(title = "Average Leaf Weight Over
Time",
x = "Days after planting (DAP)",
y = "Average Leaf Weight (g)") #
add labels

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ggplot2

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ggplot2 yacon

Create the Base Plot

# create the base scatter plot
ggplot(yacon, aes(x = stalks,
y = FOS)) +
geom_point()

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ggplot2 yacon

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ggplot2 yacon
ggplot(yacon, aes(x = stalks,
y = FOS)) +
geom_point() +
labs(title = "FOS vs Stalk Count",
x = "Number of Stalks",
y = "FOS (%)") # add labels

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ggplot2 yacon
ggplot(yacon, aes(x = stalks,
y = FOS)) +
geom_point(color = "darkgreen") + #
change color of points
labs(title = "FOS vs Stalk Count",
x = "Number of Stalks",
y = "FOS (%)") # add labels

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ggplot2 yacon
ggplot(yacon, aes(x = stalks,
y = FOS,
color = entry)) + #
color by grouping variable (entry)
geom_point() +
labs(title = "FOS vs Stalk Count",
x = "Number of Stalks",
y = "FOS (%)") # add labels

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ggplot2 yacon
ggplot(yacon, aes(x = stalks,
y = FOS,
color = entry)) + #
color by grouping variable (entry)
geom_point() +
labs(title = "FOS vs Stalk Count",
x = "Number of Stalks",
y = "FOS (%)") + # add labels
scale_color_manual(values =
c("maroon", "forestgreen", "sienna",
"tomato", "steelblue", "mediumorchid",
"rosybrown", "orange"))

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ggplot2 yacon
# load required package
library(RColorBrewer)

ggplot(yacon, aes(x = stalks,

y = FOS,
color = entry)) + #
color by grouping variable (entry)
geom_point() +
labs(title = "FOS vs Stalk Count",
x = "Number of Stalks",
y = "FOS (%)") + # add labels
scale_color_brewer(palette = "Dark2")
# use a pre-defined color palette from
RColorBrewer

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ggplot2

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ggplot2
library(RColorBrewer)
ggplot(yacon, aes(x = stalks,
y = FOS,
color = entry)) + #
color by grouping variable (entry)
geom_point() +
labs(title = "FOS vs Stalk Count",
x = "Number of Stalks",
y = "FOS (%)") + # add labels
scale_color_brewer(palette = "Dark2")
+
theme_classic() # apply classic theme

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ggplot2
library(RColorBrewer)
ggplot(yacon, aes(x = stalks,
y = FOS,
color = entry)) + #
color by grouping variable (entry)
geom_point() +
labs(title = "FOS vs Stalk Count",
x = "Number of Stalks",
y = "FOS (%)") + # add labels
scale_color_brewer(palette = "Dark2")
+
theme_light() # apply light theme

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ggplot2
library(RColorBrewer)
ggplot(yacon, aes(x = stalks,
y = FOS,
color = entry)) + #
color by grouping variable (entry)
geom_point() +
labs(title = "FOS vs Stalk Count",
x = "Number of Stalks",
y = "FOS (%)") + # add labels
scale_color_brewer(palette = "Dark2")
+
theme_minimal() # apply minimal theme

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ggplot2
library(RColorBrewer)
ggplot(yacon, aes(x = stalks,
y = FOS,
color = entry)) + #
color by grouping variable (entry)
geom_point() +
labs(title = "FOS vs Stalk Count",
x = "Number of Stalks",
y = "FOS (%)") + # add labels
scale_color_brewer(palette = "Dark2")
+
theme_bw() # apply classic theme

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ggplot2
• useful for creating multi-panel plots by grouping data
• uses the functions:
facet_wrap()
facet_grid()

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ggplot2 facet_wrap()
ggplot(yacon, aes(x = stalks,
y = FOS,
color = entry)) +
geom_point() +
labs(title = "FOS vs Stalk Count",
x = "Number of Stalks",
y = "FOS (%)") +
scale_color_brewer(palette = "Dark2")
+
theme_bw() +
facet_wrap(~locality) # creates a
panel for each location

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ggplot2 facet_wrap()
ggplot(yacon, aes(x = stalks,
y = FOS,
color = entry)) +
geom_point() +
labs(title = "FOS vs Stalk Count",
x = "Number of Stalks",
y = "FOS (%)") +
scale_color_brewer(palette = "Dark2")
+
theme_bw() +
facet_wrap(~locality, ncol=1) # stacks
panels in a column

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ggplot2 facet_grid
ggplot(yacon, aes(x = stalks,
y = FOS,
color = entry)) +
geom_point() +
labs(title = "FOS vs Stalk Count",
x = "Number of Stalks",
y = "FOS (%)") +
scale_color_brewer(palette = "Dark2")
+
theme_bw() +
facet_grid(dose~locality) # creates a
panel for each dose x location

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agricolae

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agricolae
• provides functions for experimental design and analysis of
agricultural experiments
• planning of field experiments
General Syntax
design.<design_type>(trt, r, serie, seed)

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agricolae
# create a vector defining your treatments
treatment <- c("A", "B", "C")
# create CRD layout with 10 replicates per treatment level
design_crd <- design.crd(treatment, r=10, seed=123, serie=2)
# extract the design book
book_crd <- design_crd$book
# view first 3 rows of the design book
head(book_crd, 3)

## plots r treatment
## 1 101 1 C
## 2 102 1 A
## 3 103 2 A

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agricolae
# create a vector defining your treatments
treatment <- c("A", "B", "C", "D", "E")

# set number of replicates

rep = 4

# create RCBD layout

design_rcbd <- design.rcbd(treatment, rep, seed=123, serie=2)

# apply zigzag layout

book_rcbd<- zigzag(design_rcbd) #serpentine layout

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agricolae
# display RCBD layout
print(design_rcbd$sketch)
## [,1] [,2] [,3] [,4] [,5]
## [1,] "A" "C" "D" "E" "B"
## [2,] "B" "A" "E" "C" "D"
## [3,] "A" "D" "B" "E" "C"
## [4,] "E" "C" "D" "B" "A"
# display plot numbers
print(matrix(book_rcbd[,1],byrow = TRUE, ncol = 5))
## [,1] [,2] [,3] [,4] [,5]
## [1,] 101 102 103 104 105
## [2,] 205 204 203 202 201
## [3,] 301 302 303 304 305
## [4,] 405 404 403 402 401
# save the design to a csv file
write.csv(book_rcbd, "book_rcbd.csv", row.names=FALSE)

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agricolae
# create a vector for your treatments
treatment <- c("A", "B", "C", "D")

# generate LSD layout using specified treatments

design_lsd <- design.lsd(treatment, seed=123, serie=2)

# display the LSD layout

print(design_lsd$sketch)
## [,1] [,2] [,3] [,4]
## [1,] "C" "A" "B" "D"
## [2,] "B" "D" "A" "C"
## [3,] "D" "B" "C" "A"
## [4,] "A" "C" "D" "B"

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agricolae
# apply zigzag plot numbering to the design layout
book_lsd <- zigzag(design_lsd)

# display the plot layout in a 4-column matrix

print(matrix(book_lsd[,1],byrow = TRUE, ncol = 4))
## [,1] [,2] [,3] [,4]
## [1,] 101 102 103 104
## [2,] 204 203 202 201
## [3,] 301 302 303 304
## [4,] 404 403 402 401
# save the design to a CSV file
write.csv(book_lsd, "book_rcbd.csv", row.names=FALSE)

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agricolae
• design.ab(): factorial experiments
• design.split(): split-plot experiments
• design.strip(): strip-plot experiments
• design.alpha(): alpha-lattice experiments

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agricolae
data(yacon) # load the built-in dataset
head(yacon, 3) # display first 3 rows
## entry replication roots
## 1 P1385 1 21.9
## 2 P1385 2 21.3
## 3 P1385 3 21.8

# declare categorical variables as factors

yacon$entry <- as.factor(yacon$entry)
yacon$block <- as.factor(yacon$replication)

# define your model

model <- aov(roots ~ block + entry, data = yacon)

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agricolae
# display anova table
summary(model)

## Df Sum Sq Mean Sq F value Pr(>F)

## block 2 1.18 0.590 1.747 0.21
## entry 7 48.37 6.909 20.440 2.47e-06 ***
## Residuals 14 4.73 0.338
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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agricolae
# perform Tukey HSD test
hsd_result <- HSD.test(model, "entry", group = TRUE)

# view groupings
print(hsd_result$groups)

## roots groups
## AMM5150 23.03333 a
## AKW5075 22.43333 a
## AMM5163 22.16667 ab
## P1385 21.66667 ab
## AMM5136 20.73333 bc
## ARB5125 19.63333 c
## SAL136 19.43333 c
## CLLUNC118 19.06667 c

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• Use the function and help operator

help(ggplot)
?geom_boxplot
??geom_point
• Refer to package documentations
• Data visualization: https://r-graph-gallery.com/

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HORT 299/399 Special Seminar

An Introduction to
Data Analysis &
Visualization Using R

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