Introduction to GGplot2

Anne Segonds-Pichon, Simon Andrews

v2021-09
Plotting figures and graphs with ggplot
• ggplot is the plotting library for tidyverse
• Powerful
• Flexible

• Follows the same conventions as the rest of tidyverse

• Data stored in tibbles
• Data is arranged in 'tidy' format
• Tibble is the first argument to each function
Code structure of a ggplot graph
• Start with a call to ggplot()
• Pass the tibble of data (normally via a pipe)
• Say which columns you want to use via a call to aes()

• Say which graphical representation (geometry) you want to use

• Points, lines, barplots etc

• Customise labels, colours annotations etc.

Geometries and Aesthetics
• Geometries are types of plot
geom_point() Point geometry, (x/y plots, stripcharts etc)
geom_line() Line graphs
geom_boxplot() Box plots
geom_col() Barplots
geom_histogram() Histogram plots

• Aesthetics are graphical parameters which can be adjusted in a given

geometry
Aesthetics for geom_point()
How do you define aesthetics
• Fixed values
• Colour all points red
• Make the points size 4

• Encoded from your data – called an aesthetic mapping

• Colour according to genotype
• Size based on the number of observations

• Aesthetic mappings are set using the aes() function, normally as an

argument to the ggplot function

data %>% ggplot(aes(x=weight, y=height, colour=genotype))

Our first plot…
ggplot(expression, aes(x=WT, y=KO)) + geom_point()
> expression
• Identify the tibble with
# A tibble: 12 x 4
the data you want to plot
Gene WT KO pValue
<chr> <dbl> <dbl> <dbl> • Decide on the geometry
1 Mia1 5.83 3.24 0.1 (plot type) you want to
2 Snrpa 8.59 5.02 0.001 use
3 Itpkc 8.49 6.16 0.04 • Decide which columns will
4 Adck4 7.69 6.41 0.2 modify which aesthetic
5 Numbl 8.37 6.81 0.1
6 Ltbp4 6.96 10.4 0.001
7 Shkbp1 7.57 5.83 0.1 • Call
8 Spnb4 10.7 9.38 0.2 ggplot(aes(…..))
9 Blvrb 7.32 5.29 0.05 • Add a geom_xxx
10 Pgam1 0 0.285 0.5 function call
11 Sertad3 8.13 3.02 0.0001
12 Sertad1 7.69 4.34 0.01
Our second plot…
ggplot(expression, aes(x=WT, y=KO)) + geom_line()
> expression
# A tibble: 12 x 4
Gene WT KO pValue
<chr> <dbl> <dbl> <dbl>
1 Mia1 5.83 3.24 0.1
2 Snrpa 8.59 5.02 0.001
3 Itpkc 8.49 6.16 0.04
4 Adck4 7.69 6.41 0.2
5 Numbl 8.37 6.81 0.1
6 Ltbp4 6.96 10.4 0.001
7 Shkbp1 7.57 5.83 0.1
8 Spnb4 10.7 9.38 0.2
9 Blvrb 7.32 5.29 0.05
10 Pgam1 0 0.285 0.5
11 Sertad3 8.13 3.02 0.0001
12 Sertad1 7.69 4.34 0.01
Our third plot…
expression %>%
ggplot (aes(x=WT, y=KO)) +
geom_point(colour="red2", size=5)
Exercise 1
More Geometries
Other Geometries
• Barplots • Distribution Summaries
• geom_bar • geom_histogram
• geom_col • geom_density
• geom_violin
• geom_boxplot
• Stripcharts
• geom_jitter
Drawing a barplot (geom_col() or
geom_bar())
• Two different functions – depends on the nature of the data

• If your data has values which represents the height of the bars use
geom_col

• If your data has individual values and you want the plot to either count them
or calculate a quantitative summary (usually the mean) then use geom_bar

• Many geometries are “summarising geometries”. They calculate one or

more aesthetics for you.
Drawing a bar height barplot (geom_col())
• Plot the expression values for the
WT samples for all genes

• What is your X?
• What is your Y?

> expression
# A tibble: 12 x 4
Gene WT KO pValue
<chr> <dbl> <dbl> <dbl>
1 Mia1 5.83 3.24 0.1
2 Snrpa 8.59 5.02 0.001
A bar height barplot > expression
# A tibble: 12 x 4
Gene WT KO pValue
<chr> <dbl> <dbl> <dbl>
expression %>% 1 Mia1 5.83 3.24 0.1
2 Snrpa 8.59 5.02 0.001
ggplot(aes(x=Gene, y=WT)) +
geom_col()
A count summary barplot (geom_bar)
mutation.plotting.data %>%
ggplot(aes(x=mutation)) +
geom_bar()

> mutation.plotting.data
# A tibble: 24,686 x 9
CHR POS dbSNP mutation
<chr> <dbl> <chr> <chr>
1 1 69270 . A->G
2 1 69511 rs75062661 A->G
3 1 69761 . A->T
4 1 69897 rs75758884 T->C
5 1 877831 rs6672356 T->C
6 1 881627 rs2272757 G->A
 A mean summary barplot (geom_bar)
mutation.plotting.data %>%
ggplot(aes(x=mutation, y=MutantReads)) +
geom_bar(stat="summary", fun=mean)

> mutation.plotting.data
# A tibble: 24,686 x 9
CHR POS mutation MutantReads
<chr> <dbl> <chr> <dbl>
1 1 69270 A->G 3
2 1 69511 A->G 24
3 1 69761 A->T 8
4 1 69897 T->C 3
5 1 877831 T->C 10
6 1 881627 G->A 52
7 1 887801 A->G 47
8 1 888639 T->C 23
9 1 888659 T->C 17
10 1 889158 G->C 25
 Stacked and Grouped Barplots
bar.group %>%
ggplot(aes(x=Gene, y=value)) +
geom_col()

> bar.group
# A tibble: 12 x 3
Gene genotype value
<chr> <chr> <dbl>
1 Gnai3 WT 9.39
2 Pbsn WT 91.7
3 Cdc45 WT 69.2
4 Gnai3 WT 10.9
5 Pbsn WT 59.6
6 Cdc45 WT 36.1
7 Gnai3 KO 33.5
8 Pbsn KO 45.3
9 Cdc45 KO 54.4
10 Gnai3 KO 81.9
11 Pbsn KO
12 Cdc45 KO
82.3
38.1 Sum of values
 Stacked and Grouped Barplots
bar.group %>%
ggplot(aes(x=Gene, y=value, fill=genotype)) +
geom_col()

> bar.group
# A tibble: 12 x 3
Gene genotype value
<chr> <chr> <dbl>
1 Gnai3 WT 9.39
2 Pbsn WT 91.7
3 Cdc45 WT 69.2
4 Gnai3 WT 10.9
5 Pbsn WT 59.6
6 Cdc45 WT 36.1
7 Gnai3 KO 33.5
8 Pbsn KO 45.3
9 Cdc45 KO 54.4
10 Gnai3 KO 81.9
11 Pbsn KO
12 Cdc45 KO
82.3
38.1 Stacked Sums
 Stacked and Grouped Barplots
bar.group %>%
ggplot(aes(x=Gene, y=value, fill=genotype)) +
geom_col(position="dodge")

> bar.group
# A tibble: 12 x 3
Gene genotype value
<chr> <chr> <dbl>
1 Gnai3 WT 9.39
2 Pbsn WT 91.7
3 Cdc45 WT 69.2
4 Gnai3 WT 10.9
5 Pbsn WT 59.6
6 Cdc45 WT 36.1
7 Gnai3 KO 33.5
8 Pbsn KO 45.3
9 Cdc45 KO 54.4
10 Gnai3 KO 81.9
11 Pbsn KO
12 Cdc45 KO
82.3
38.1 Individual values
Plotting distributions - histograms
> many.values
# A tibble: 100,000 x 2
values genotype
<dbl> <chr>
1 1.90 KO
2 2.39 WT
3 4.32 KO
4 2.94 KO
5 0.728 WT
6 -0.280 WT
7 0.337 WT
8 -1.31 WT
9 1.55 WT
10 1.86 KO

many.values %>%
ggplot(aes(x=values)) +
geom_histogram(binwidth = 0.1, fill="yellow", colour="black")
Plotting distributions - density
> many.values
# A tibble: 100,000 x 2
values genotype
<dbl> <chr>
1 1.90 KO
2 2.39 WT
3 4.32 KO
4 2.94 KO
5 0.728 WT
6 -0.280 WT
7 0.337 WT
8 -1.31 WT
9 1.55 WT
10 1.86 KO

many.values %>%
ggplot(aes(x=values, fill=genotype)) +
geom_density(colour="black", alpha=0.5)
Plotting distributions – violin plots
> many.values
# A tibble: 100,000 x 2
values genotype
<dbl> <chr>
1 1.90 KO
2 2.39 WT
3 4.32 KO
4 2.94 KO
5 0.728 WT
6 -0.280 WT
7 0.337 WT
8 -1.31 WT
9 1.55 WT
10 1.86 KO

many.values %>%
ggplot(aes(x=genotype, y=values)) +
geom_violin(colour="black", fill="yellow")
Plotting distributions – boxplots
> many.values
# A tibble: 100,000 x 2
values genotype
<dbl> <chr>
1 1.90 KO
2 2.39 WT
3 4.32 KO
4 2.94 KO
5 0.728 WT
6 -0.280 WT
7 0.337 WT
8 -1.31 WT
9 1.55 WT
10 1.86 KO

many.values %>%
ggplot(aes(x=genotype, y=values)) +
geom_boxplot(colour="black", fill="yellow")
Plotting distributions – stripcharts
> many.values
# A tibble: 100,000 x 2
values genotype
<dbl> <chr>
1 1.90 KO
2 2.39 WT
3 4.32 KO
4 2.94 KO
5 0.728 WT
6 -0.280 WT
7 0.337 WT
8 -1.31 WT
9 1.55 WT
10 1.86 KO

many.values %>%
group_by(genotype) %>%
sample_n(100) %>%
ggplot(aes(x=genotype, y=values)) +
geom_jitter(height=0, width = 0.3)
Exercise 2
Annotation, Scaling and Colours
Titles and axis labels
• Can add calls to functions to set them individually
• ggtitle("Main title")
• xlab("X axis")
• ylab("Y axis")

• Can set them all together with labs()

• title="Main title"
• x="X axis"
• y="Y axis"
Changing scaling
• Alter the data before plotting
• mutate(value=log(value))

• Alter the data whilst plotting

• ggplot(aes(x=log(value)))

• Alter the scale of the plot

• Add an option to adjust the scaling of the axis
 Axis scaling options
• Transforming scales • Adjusting ranges
• scale_x_log10() • scale_x_continuous()
• scale_x_sqrt() • limits=c(-5,5)
• scale_x_reverse() • breaks=seq(from=-5,by=2,to=5)
• minor_breaks
Equivalent _y_ versions also exist
• labels

• Switching axes • coord_cartesian()

• coord_flip() • xlim=c(-5,5)
• ylim=c(10,20)
Annotation and scaling example
trumpton %>%
ggplot(aes(x=Age, y=Weight))+
geom_point() +

xlab("Age (Years)")+
ylab("Weight (kg)")+
ggtitle("How heavy are firemen?")+

coord_cartesian(
xlim=c(0,50),
ylim=c(80,110)
)
ggPlot Themes

• theme_grey()
• theme_bw()
• theme_dark()
• theme_light()
• theme_minimal()
• theme_classic()
• theme_linedraw()
Setting and Customising themes
• Globally
theme_set(theme_bw(base_size=14))

• In a single plot
+theme_dark()
Customising themes

theme_update(plot.title = element_text(hjust = 0.5))

plot + theme(plot.title = element_text(hjust = 0.5))

theme(line, rect, text, title, aspect.ratio, axis.title, axis.title.x, axis.title.x.top, axis.title.x.bottom,

axis.title.y, axis.title.y.left,axis.title.y.right, axis.text, axis.text.x, axis.text.x.top,
axis.text.x.bottom, axis.text.y, axis.text.y.left, axis.text.y.right, axis.ticks, axis.ticks.x,
axis.ticks.x.top, axis.ticks.x.bottom, axis.ticks.y, axis.ticks.y.left, axis.ticks.y.right,
axis.ticks.length, axis.line, axis.line.x, axis.line.x.top, axis.line.x.bottom, axis.line.y,
axis.line.y.left, axis.line.y.right, legend.background, legend.margin, legend.spacing, legend.spacing.x,
legend.spacing.y, legend.key, legend.key.size, legend.key.height, legend.key.width, legend.text,
legend.text.align, legend.title, legend.title.align, legend.position, legend.direction, legend.justification,
legend.box, legend.box.just, legend.box.margin, legend.box.background, legend.box.spacing, panel.background,
panel.border, panel.spacing, panel.spacing.x, panel.spacing.y, panel.grid, panel.grid.major,
panel.grid.minor, panel.grid.major.x, panel.grid.major.y, panel.grid.minor.x, panel.grid.minor.y,
panel.ontop, plot.background, plot.title, plot.subtitle, plot.caption, plot.tag, plot.tag.position,
plot.margin, strip.background, strip.background.x, strip.background.y, strip.placement, strip.text,
strip.text.x, strip.text.y, strip.switch.pad.grid, strip.switch.pad.wrap)
https://ggplot2.tidyverse.org/reference/theme.html
Theme setting example
theme_set(theme_bw(base_size = 14))
theme_update(plot.title = element_text(hjust=1))

OR

my.plot +
theme_bw(base_size = 14) +
theme(plot.title = element_text(hjust=1))
Changing Quantitative Colours
storms %>%
ggplot(aes(x=lat, y=long, colour=wind)) +
geom_point()
Changing Plotting Order
storms %>% storms %>%
ggplot(aes(x=lat,y=long,colour=wind))+ arrange(wind) %>%
geom_point() ggplot(aes(x=lat,y=long,colour=wind))+
geom_point()
Changing Quantitative Colours
storms %>%
arrange(wind) %>%
ggplot(aes(x=lat, y=long, colour=wind))+
geom_point() +
scale_colour_gradient(low="lightgrey", high="blue")
Changing Quantitative Colours
storms %>%
arrange(wind) %>%
ggplot(aes(x=lat, y=long, colour=wind))+
geom_point() +
scale_colour_gradientn(colours=c("blue","green2","red","yellow"))
ColorBrewer Scales

Quantitative
scale_colour_distiller

Categorical
scale_colour_brewer
Changing Quantitative Colours
storms %>%
arrange(wind) %>%
ggplot(aes(x=lat, y=long, color=wind))+
geom_point() +
scale_color_distiller(palette="Reds", direction = 1)
Changing Categorical Colours
storms %>%
filter(year==1983) %>%
ggplot(aes(x=wind, y=pressure, colour=status)) +
geom_point(size=3)
Changing Categorical Colours
storms %>%
filter(year==1983) %>%
ggplot(aes(x=wind,y=pressure, colour=status)) +
geom_point(size=3) +
scale_colour_manual(values =
c("orange","purple","green2"))
Changing Categorical Colours
storms %>%
filter(year==1983) %>%
ggplot(aes(x=wind,y=pressure, colour=status)) +
geom_point(size=3) +
scale_colour_brewer(palette="Set1")
Categorical Colour Ordering

# A tibble: 10,010 x 6
lat long status category wind pressure
<dbl> <dbl> <chr> <ord> <int> <int>
1 27.5 -79 tropical depression -1 25 1013
2 28.5 -79 tropical depression -1 25 1013
3 29.5 -79 tropical depression -1 25 1013
4 30.5 -79 tropical depression -1 25 1013
5 31.5 -78.8 tropical depression -1 25 1012
6 32.4 -78.7 tropical depression -1 25 1012
7 33.3 -78 tropical depression -1 25 1011
8 34 -77 tropical depression -1 30 1006
9 34.4 -75.8 tropical storm 0 35 1004
10 34 -74.8 tropical storm 0 40 1002
# ... with 10,000 more rows

Status is a character vector – ordering is alphabetical

Factors
• Similar to text (character) vectors, but with some differences
• They have controlled values – you can limit which values can be added
• The values which can go in are tracked separately to the data
• The values which can go in have an explicit order

• GGplot respects the ordering of factors, so converting to factors is the

simplest way to re-order a plot
Converting character vectors to factors
> chr.names
[1] "simon" "anne" "laura" "felix" "simon" "anne" "laura"
[8] "felix" "simon" "anne" "laura" "felix" "simon" "anne"
[15] "laura" "felix" "simon" "anne" "laura" "felix"

> factor(chr.names)
[1] simon anne laura felix simon anne laura felix simon
[10] anne laura felix simon anne laura felix simon anne
[19] laura felix
Levels: anne felix laura simon

> factor(chr.names, levels=c("simon","anne","laura","felix"))

[1] simon anne laura felix simon anne laura felix simon
[10] anne laura felix simon anne laura felix simon anne
[19] laura felix
Levels: simon anne laura felix
Categorical Colour Ordering
Use factors for explicit ordering
storms %>%
mutate(
status=factor(
status,
levels=c("tropical depression","tropical storm","hurricane")
)
)

# A tibble: 10,010 x 6
lat long status category wind pressure
<dbl> <dbl> <fct> <ord> <int> <int>
1 27.5 -79 tropical depression -1 25 1013
2 28.5 -79 tropical depression -1 25 1013
3 29.5 -79 tropical depression -1 25 1013
4 30.5 -79 tropical depression -1 25 1013
Categorical Colour Ordering
storms %>%
mutate(status=factor(status, levels=c("tropical depression","tropical storm","hurricane"))) %>%
filter(year==1983) %>%
ggplot(aes(x=wind,y=pressure, colour=status)) +
geom_point(size=3)+
scale_color_brewer(palette="Set1")
 LastName FirstName Age Weight Height

Reordering example
<chr> <chr> <dbl> <dbl> <dbl>
1 Hugh Chris 26 90 175
2 Pew Adam 32 102 183

Keep the original order

3 Barney Daniel 18 88 168
4 McGrew Chris 48 97 155
5 Cuthbert Carl 28 91 188
6 Dibble Liam 35 94 145
7 Grub Doug 31 89 164

trumpton %>%
ggplot(aes(x=LastName, y=Height)) +
geom_col()

The default is to
order alphabetically
 LastName FirstName Age Weight Height

Reordering example
<chr> <chr> <dbl> <dbl> <dbl>
1 Hugh Chris 26 90 175
2 Pew Adam 32 102 183

Keep the original order

3 Barney Daniel 18 88 168
4 McGrew Chris 48 97 155
5 Cuthbert Carl 28 91 188
6 Dibble Liam 35 94 145
7 Grub Doug 31 89 164

trumpton %>%
mutate(LastName=factor(LastName, levels=LastName)) %>%
ggplot(aes(x=LastName, y=Height)) +
geom_col()

We can convert to a factor and use

levels to enforce the same order. If
we had just converted to a factor it
would have been alphabetical still.
Quantitative ordering with reorder
• The reorder function allows you to order the levels of a factor by a
different quantitative variable

• It allows you to sort a figure by value

• reorder(categorical, quantitative)
 LastName FirstName Age Weight Height
<chr> <chr> <dbl> <dbl> <dbl>
1 Hugh Chris 26 90 175

Reordering examples
2 Pew Adam 32 102 183
3 Barney Daniel 18 88 168
4 McGrew Chris 48 97 155
5 Cuthbert Carl 28 91 188
6 Dibble Liam 35 94 145
7 Grub Doug 31 89 164

trumpton %>%
mutate(LastName=reorder(LastName,Height)) %>%
ggplot(aes(x=LastName, y=Height)) +
geom_col()

By using reorder we can make the

levels correspond to a quantitative
variable. Here it is the same one we're
plotting, but it doesn't have to be.
 LastName FirstName Age Weight Height
<chr> <chr> <dbl> <dbl> <dbl>
1 Hugh Chris 26 90 175

Reordering examples
2 Pew Adam 32 102 183
3 Barney Daniel 18 88 168
4 McGrew Chris 48 97 155
5 Cuthbert Carl 28 91 188
6 Dibble Liam 35 94 145
7 Grub Doug 31 89 164

trumpton %>%
mutate(LastName=reorder(LastName,-Height)) %>%
ggplot(aes(x=LastName, y=Height)) +
geom_col()

We can use -Height in the reorder to

reverse the sorting order
Exercise 3
Statistical Overlays
Overlaying raw data and summaries
many.values %>%
group_by(genotype) %>%
sample_n(100) %>%
ggplot(aes(x=genotype, y=values)) +
geom_jitter(height=0, width = 0.3)
Overlaying raw data and summaries
many.values %>%
group_by(genotype) %>%
sample_n(100) %>%
ggplot(aes(x=genotype, y=values)) +
geom_jitter(height=0, width = 0.3) +
geom_boxplot()
Overlaying raw data and summaries
many.values %>%
group_by(genotype) %>%
sample_n(100) %>%
ggplot(aes(x=genotype, y=values)) +
geom_boxplot(size=1.5, colour="grey") +
geom_jitter(height=0, width = 0.3)
Stat Summary
• Add summary statistics to discrete data

• Main options
• geom – how is this going to be displayed
• pointrange (default)
• errorbar
• linerange
• Crossbar

• fun.data
• Function to produce
• Min, Centre, Max
• Eg mean_se, mean_cl_boot, mean_cl_normal,mean_sdl

• Can also use fun.min, fun, fun.max separately

Overlaying raw data and summaries
many.values %>%
group_by(genotype) %>%
sample_n(10) %>%
ggplot(aes(x=genotype, y=values)) +
geom_jitter(height=0, width = 0.3) +
stat_summary(
geom="crossbar",
fun.data=mean_se,
size=1, alpha=0, colour="grey"
)
Overlaying raw data and summaries
many.values %>%
group_by(genotype) %>%
sample_n(10) %>%
ggplot(aes(x=genotype, y=values)) +
geom_jitter(height=0, width = 0.3) +
stat_summary(
geom="errorbar",
fun = mean,
fun.max = mean,
fun.min = mean,
size=2,
colour="grey"
)
 Overlaying raw data and summaries
group.data %>%
ggplot(aes(x=Sex, y=Height)) +
geom_bar(stat="summary", fun=mean) +
stat_summary(geom="errorbar", width=0.4, size=2)

NB The fun=mean in geom_bar is optional since that’s the default

 Using pre-calculated variance measures
data.with.stdev %>%
ggplot(aes(x=species,y=height, ymin=height-stdev, ymax=height+stdev)) +
geom_col(fill="yellow", color="black") +
geom_errorbar(width=0.4)

> data.with.stdev
# A tibble: 3 x 3
species height stdev
<chr> <dbl> <dbl>
1 Human 160 30
2 Dog 50 20
3 Mouse 5 2
Adding Reference / Regression Lines
• geom_hline – Adds a horizontal line (specify yintercept)
• geom_vline – Adds a vertical line (specify xintercept)

• geom_abline – Adds an angled line (specify slope and intercept)

• Values can come from the lm function to generate a linear model
• geom_smooth – Calculates and draws regression lines
• Loess smoothed curves
• Linear modelled lines
Trend lines
trend_data %>% trend_data %>%
ggplot(aes(x=trend,y=noise+trend)) + ggplot(aes(x=trend,y=noise+trend)) +
geom_point() + geom_point() +
geom_hline( geom_hline(
yintercept=5, size=1, colour="red2") + yintercept=5, size=1, colour="red2")
geom_smooth(size=1.5) geom_smooth(size=1.5, method="lm")
Exercise 4
Faceting and
Highlighting
Faceting
• Faceting allows you to take a single graph definition and create
multiple graphs of the same type based on additional categorical
factors

• facet_grid draws graphs in rows and columns based on 1 or 2

factors

• facet_wrap draws a 2D arrangement of graphs based on a single

factor
Faceting – using facet_wrap()
child.variants %>%
ggplot(aes(x=MutantReadPercent, fill=CHR)) +
geom_density()
Faceting – using facet_wrap()
child.variants %>%
ggplot(aes(x=MutantReadPercent)) +
geom_density(fill="red2") +
facet_wrap(vars(CHR))

Note that the variable defining the facets

must be passed through the vars() function
Faceting – using facet_grid()
group.data %>%
ggplot(aes(x=Height, y=Length)) +
geom_point(size=6, color="red2") +
facet_grid(
rows=vars(Genotype),
cols=vars(Sex)
)

Note that the variable defining the facets

must be passed through the vars() function
Selective Overlays and
Highlighting
 # A tibble: 87 x 4
name height mass homeworld

Selective highlighting <chr>

1 Luke Skywalker
2 C-3PO
<int> <dbl> <chr>
172
167
77 Tatooine
75 Tatooine
3 R2-D2 96 32 Naboo
starwars %>% 4 Darth Vader 202 136 Tatooine

ggplot(aes(x=height,y=log(mass), label=name))+
geom_point() +
geom_text(vjust=1.5)
Selective highlighting
> famous
[1] "Yoda" "Darth Vader" "Chewbacca" "Han Solo" "R2-D2" "Luke Skywalker" "Leia Organa"

starwars %>%
filter(name %in% famous) -> starwars.famous

starwars %>%
ggplot(aes(x=height,y=log(mass),label=name))+
geom_point(col="lightgrey") +
geom_text(data=starwars.famous)+
geom_point(data=starwars.famous, color="red2")
Selective highlighting
Selective highlighting - ggrepel
library(ggrepel)

starwars %>%
ggplot(aes(x=height,y=log(mass),label=name))+
geom_point(col="lightgrey") +
geom_text_repel(data=starwars.famous)+
geom_point(data=starwars.famous, color="red2")
Annotation
• The annotate function allows you to add geometries with data not
coming from the original tibble

• An easy way to put small additions (usually text) on your plot

• Aesthetic mappings are set by arguments to annotate
• Values can be multi-element vectors (unlike fixed aesthetics)
• Use the geom argument to say which geometry to use
Annotation
data %>%
ggplot(aes(x=x,y=y)) +
geom_point() +
geom_abline(slope = 3, intercept=0, size=2, colour="grey") +
annotate(geom="text",x=350,y=280,label="R^2=0.96", size=10)
Saving plots
• Operates on the last drawn plot by
default

ggsave(
filename = "test.svg",
device = "svg",
width = 6,
height = 6
)
Saving complex plots

library(ggrastr)

up_down %>%
ggplot(aes(x=Condition1,y=Condition2)) +
rasterise(
geom_point(color=up_down$colour, size=0.7),
dpi=150
) -> mixplot

ggsave("mixplot.svg", plot=mixplot, device="svg", width=6, height=6)

Exercise 5