Labels and Annotations

# Labels and Annotations
### Derek Ogle, May 2020

---

# Today's Goal

<font size="7">Describe how to modify labels (geoms and scales) and add annotations.</font>

---

# Labels

---

# Titles, Subtitles, and Captions

- Added with `labs()`.

--
  - `title=` adds a main title at the top (stats above y-axis).
  - `subtitle=` adds a subtitle below the main title.
  - `caption=` adds a "caption" to the bottom-right.
  - `tag=` adds tag label to the very top-left.

<img src="Lecture_Annotations_files/figure-html/labs-1.png" width="40%" />
]

---

# Example

---

# Background

- Isle Royale Moose and Wolves.
  - Note an outbreak of parvovirus occurred in 1980.

```r
## #!# Set to your own working directory and have just your filename below.
irmw <- read.csv("https://raw.githubusercontent.com/droglenc/NCData/master/WolvesMoose_IsleRoyale_June2019.csv",
                 na.strings=c("NA","N/A"))  %>%
  select(year,wolves,moose) %>%
  mutate(parvo=ifelse(year>1980,"Post-parvo","Pre-parvo"),
         parvo=factor(parvo,levels=c("Pre-parvo","Post-parvo")))
head(irmw)
```

```
  year wolves moose     parvo
1 1959     20   538 Pre-parvo
2 1960     22   564 Pre-parvo
3 1961     22   572 Pre-parvo
4 1962     23   579 Pre-parvo
5 1963     20   596 Pre-parvo
6 1964     26   620 Pre-parvo
```

---

```r
*ggplot(data=irmw,mapping=aes(x=year,y=wolves)) +
* geom_line(color="gray70") +
* geom_point(aes(fill=parvo),size=1.25,pch=21) +
* scale_fill_manual(values=c("Pre-parvo"="white","Post-parvo"="black")) +
* scale_y_continuous(limits=c(0,NA),expand=expansion(mult=c(0,0.04))) +
* scale_x_continuous(expand=expansion(mult=0.04)) +
* theme_bw() +
* theme(panel.grid.minor=element_blank())
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw1_user_1_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
ggplot(data=irmw,mapping=aes(x=year,y=wolves)) +  
  geom_line(color="gray70") +  
  geom_point(aes(fill=parvo),size=1.25,pch=21) +  
  scale_fill_manual(values=c("Pre-parvo"="white","Post-parvo"="black")) +  
  scale_y_continuous(limits=c(0,NA),expand=expansion(mult=c(0,0.04))) +  
  scale_x_continuous(expand=expansion(mult=0.04)) +  
  theme_bw() +  
  theme(panel.grid.minor=element_blank()) +  
* labs(title="Number of Wolves on Isle Royale, 1959-2019",
*      subtitle="Estimated from aerial counts",
*      caption="Source: https://isleroyalewolf.org")
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw1_user_2_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
ggplot(data=irmw,mapping=aes(x=year,y=wolves)) +  
  geom_line(color="gray70") +  
  geom_point(aes(fill=parvo),size=1.25,pch=21) +  
  scale_fill_manual(values=c("Pre-parvo"="white","Post-parvo"="black")) +  
  scale_y_continuous(limits=c(0,NA),expand=expansion(mult=c(0,0.04))) +  
  scale_x_continuous(expand=expansion(mult=0.04)) +  
  theme_bw() +  
  theme(panel.grid.minor=element_blank()) +  
  labs(title="Number of Wolves on Isle Royale, 1959-2019",  
       subtitle="Estimated from aerial counts",  
       caption="Source: https://isleroyalewolf.org") +  
* labs(x=element_blank(),
*      y=element_blank(),
*      fill="Relative to Parvo")
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw1_user_3_output-1.png" width="100%" />
]]

---

# Annotations

---

# Annotation Layers

- Add `geom_` ... but aesthetics not mapped from variables in a data.frame.

--
  - Aesthetics passed in as single values or small vectors.
  - Useful for adding small annotations (such as text labels or segments).

&nbsp;

--
- Use `annotate()`.

--
  - `geom=` (first argument) is the `geom_` to use.

--
  - Remaining arguments are position aesthetics (e.g., `x=`, `y=`, `xmin=`, `xmax=`, `ymin=`, `ymax=`, `xend=`, `yend=`) ...
  
--
  - ... and other aesthetics (e.g., `color=`, `fill=`, `size=`).

---

# Example

---

```r
p <- ggplot(data=irmw,mapping=aes(x=year,y=wolves)) +  
  geom_line(color="gray70") +  
  geom_point(aes(fill=parvo),size=1.25,pch=21) +  
  scale_fill_manual(values=c("Pre-parvo"="white","Post-parvo"="black")) +  
  scale_y_continuous(limits=c(0,NA),expand=expansion(mult=c(0,0.04))) +  
  scale_x_continuous(expand=expansion(mult=0.04)) +  
  theme_bw() +  
  theme(panel.grid.minor=element_blank(),legend.position="none") +  
  labs(title="Number of Wolves on Isle Royale, 1959-2019",  
       subtitle="Estimated from aerial counts",  
       caption="Source: https://isleroyalewolf.org",  
       x=element_blank(),y=element_blank())  
 
p
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw2_1_1_output-1.png" width="100%" />
]]

---

```r
p1 <- p   
 
p1
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw2a_non_seq_1_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p1 <- p +  
* annotate(geom="label",x=1990,y=48,hjust="left",
*          label="Outbreak of parvovirus in 1980")
 
p1
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw2a_non_seq_2_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p1 <- p +  
  annotate(geom="label",x=1990,y=48,hjust="left",  
           label="Outbreak of parvovirus in 1980") +  
* annotate(
*   geom="segment",x=1990,y=48,xend=1980.5,yend=50,
  )  
 
p1
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw2a_non_seq_3_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p1 <- p +  
  annotate(geom="label",x=1990,y=48,hjust="left",  
           label="Outbreak of parvovirus in 1980") +  
  annotate(  
    geom="segment",x=1990,y=48,xend=1980.5,yend=50,  
*   size=0.25,
  )  
 
p1
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw2a_non_seq_4_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p1 <- p +  
  annotate(geom="label",x=1990,y=48,hjust="left",  
           label="Outbreak of parvovirus in 1980") +  
  annotate(  
    geom="segment",x=1990,y=48,xend=1980.5,yend=50,  
    size=0.25,  
*   arrow=arrow(
*     length=unit(2,"mm"),
    )  
  )  
 
p1
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw2a_non_seq_5_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p1 <- p +  
  annotate(geom="label",x=1990,y=48,hjust="left",  
           label="Outbreak of parvovirus in 1980") +  
  annotate(  
    geom="segment",x=1990,y=48,xend=1980.5,yend=50,  
    size=0.25,  
    arrow=arrow(  
      length=unit(2,"mm"),  
*     angle=15,
    )  
  )  
 
p1
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw2a_non_seq_6_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p1 <- p +  
  annotate(geom="label",x=1990,y=48,hjust="left",  
           label="Outbreak of parvovirus in 1980") +  
  annotate(  
    geom="segment",x=1990,y=48,xend=1980.5,yend=50,  
    size=0.25,  
    arrow=arrow(  
      length=unit(2,"mm"),  
      angle=15,  
*     type="closed"
    )  
  )  
 
p1
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw2a_non_seq_7_output-1.png" width="100%" />
]]

---

```r
*p1 +
* annotate(geom="label",x=2014,y=37,hjust="right",
*          label="Wolves introduced from mainland")
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw2b_user_1_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p1 +  
  annotate(geom="label",x=2014,y=37,hjust="right",  
           label="Wolves introduced from mainland") +  
* annotate(geom="curve",x=2014,y=37,xend=2019,yend=15.5,size=0.25,
*          arrow=arrow(length=unit(2,"mm"),angle=15,type="closed"),
*          curvature=-0.25)
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw2b_user_2_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p1 +  
  annotate(geom="label",x=2014,y=37,hjust="right",  
           label="Wolves introduced from mainland") +  
  annotate(geom="curve",x=2014,y=37,xend=2019,yend=15.5,size=0.25,  
           arrow=arrow(length=unit(2,"mm"),angle=15,type="closed"),  
           curvature=-0.25) +  
* annotate(geom="segment",x=2008,xend=2013.5,y=18.5,yend=1,
*          color="steelblue")
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw2b_user_3_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p1 +  
  annotate(geom="label",x=2014,y=37,hjust="right",  
           label="Wolves introduced from mainland") +  
  annotate(geom="curve",x=2014,y=37,xend=2019,yend=15.5,size=0.25,  
           arrow=arrow(length=unit(2,"mm"),angle=15,type="closed"),  
           curvature=-0.25) +  
  annotate(geom="segment",x=2008,xend=2013.5,y=18.5,yend=1,  
           color="steelblue") +  
* annotate(geom="text",x=2003,y=8,color="steelblue",
*          label="Concerned about\ninbreeding suppression")
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irw2b_user_4_output-1.png" width="100%" />
]]

---

# Labeling Individual Points

---

# Labeling Individual Points

- Provide specific details about the data.

--
  - e.g., the actual mean.
  - e.g., letters that identify significant differences.
  - e.g., the sample size.

&nbsp;

--
- Highlight individual points.

&nbsp;

--
- Can use `geom_text()`, `geom_label()`, or `annotate()`

---

# Example ... showing means

---

```r
*sum1

*ggplot(data=sum1,mapping=aes(x=lake,y=mn)) +
* geom_bar(stat="identity",fill="gray30",alpha=0.75) +
* scale_x_discrete(name="Great Lake") +
* scale_y_continuous(name="Mean Maximum Ice Coverage (%)",
*                    limits=c(0,NA),expand=expansion(mult=c(0,0.05))) +
* theme_bw() +
* theme(panel.grid.major.x=element_blank())
```
]]
.column[.content[

```
# A tibble: 5 x 6
  lake         n    mn     s   lci   uci
  <fct>    <int> <dbl> <dbl> <dbl> <dbl>
1 Superior    47  62.3  30.3  53.4  71.2
2 Michigan    47  40.5  21.7  34.1  46.8
3 Huron       47  65.3  23.3  58.5  72.1
4 Erie        47  82.6  26.0  75.0  90.3
5 Ontario     47  30.2  19.7  24.4  36.0
```

<img src="Lecture_Annotations_files/figure-html/gli_mnsbar_user_1_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
sum1

ggplot(data=sum1,mapping=aes(x=lake,y=mn)) +  
  geom_bar(stat="identity",fill="gray30",alpha=0.75) +  
  scale_x_discrete(name="Great Lake") +  
  scale_y_continuous(name="Mean Maximum Ice Coverage (%)",  
                     limits=c(0,NA),expand=expansion(mult=c(0,0.05))) +  
  theme_bw() +  
  theme(panel.grid.major.x=element_blank()) +  
* geom_text(aes(label=round(mn,1)),vjust="bottom",nudge_y=1)
```
]]
.column[.content[

<img src="Lecture_Annotations_files/figure-html/gli_mnsbar_user_2_output-1.png" width="100%" />
]]

---

# Example ... showing significance letters

---

```r
*sum1

*ggplot(data=sum1,mapping=aes(x=lake,y=mn)) +
* geom_bar(stat="identity",fill="gray30",alpha=0.75) +
* geom_errorbar(mapping=aes(ymin=lci,ymax=uci),width=0.1) +
* scale_x_discrete(name="Great Lake") +
* scale_y_continuous(name="Mean Maximum Ice Coverage (%)",
*                    limits=c(0,NA),expand=expansion(mult=c(0,0.05))) +
* theme_bw() +
* theme(panel.grid.major.x=element_blank())
```
]]
.column[.content[

<img src="Lecture_Annotations_files/figure-html/gli_mnsbar2_user_1_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
sum1

ggplot(data=sum1,mapping=aes(x=lake,y=mn)) +  
  geom_bar(stat="identity",fill="gray30",alpha=0.75) +  
  geom_errorbar(mapping=aes(ymin=lci,ymax=uci),width=0.1) +  
  scale_x_discrete(name="Great Lake") +  
  scale_y_continuous(name="Mean Maximum Ice Coverage (%)",  
                     limits=c(0,NA),expand=expansion(mult=c(0,0.05))) +  
  theme_bw() +  
  theme(panel.grid.major.x=element_blank()) +  
* geom_text(mapping=aes(y=uci,label=c("b","a","b","c","a")),
*           vjust="bottom",nudge_y=1.5)
```
]]
.column[.content[

<img src="Lecture_Annotations_files/figure-html/gli_mnsbar2_user_2_output-1.png" width="100%" />
]]

---

# Example ... showing sample size

---

```r
*sum1

<img src="Lecture_Annotations_files/figure-html/gli_mnsbar3_user_1_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
sum1

ggplot(data=sum1,mapping=aes(x=lake,y=mn)) +  
  geom_bar(stat="identity",fill="gray30",alpha=0.75) +  
  geom_errorbar(mapping=aes(ymin=lci,ymax=uci),width=0.1) +  
  scale_x_discrete(name="Great Lake") +  
  scale_y_continuous(name="Mean Maximum Ice Coverage (%)",  
                     limits=c(0,NA),expand=expansion(mult=c(0,0.05))) +  
  theme_bw() +  
  theme(panel.grid.major.x=element_blank()) +  
  geom_text(mapping=aes(y=uci,label=c("b","a","b","c","a")),  
            vjust="bottom",nudge_y=1.5) +  
* geom_text(mapping=aes(y=0,label=paste("n =",n)),
*           vjust="bottom",nudge_y=1.5)
```
]]
.column[.content[

<img src="Lecture_Annotations_files/figure-html/gli_mnsbar3_user_2_output-1.png" width="100%" />
]]

---

# Example ... highlighting individual points

---

# Background

- Examine dynamics of Moose and Wolf abundance from 1970 to 1990.
  - Make variable with label for only every fifth year.
  - Make variables with "next year's" wolf and moose abundances.

```r
irmw2 <- irmw %>%
  filter(year>=1970,year<=1990) %>%
  mutate(year5=ifelse(year %in% seq(1970,1990,5),year,""),moose.next=c(moose[-1],NA),wolves.next=c(wolves[-1],NA))
FSA::headtail(irmw2, n=6)
```

```
   year wolves moose      parvo year5 moose.next wolves.next
1  1970     18  1045  Pre-parvo  1970       1183          20
2  1971     20  1183  Pre-parvo             1243          23
3  1972     23  1243  Pre-parvo             1215          24
4  1973     24  1215  Pre-parvo             1203          31
5  1974     31  1203  Pre-parvo             1139          41
6  1975     41  1139  Pre-parvo  1975       1070          44
16 1985     22   976 Post-parvo  1985       1014          20
17 1986     20  1014 Post-parvo             1046          16
18 1987     16  1046 Post-parvo             1116          12
19 1988     12  1116 Post-parvo             1260          12
20 1989     12  1260 Post-parvo             1315          15
21 1990     15  1315 Post-parvo  1990         NA          NA
```

---

```r
*head(irmw2)

*ggplot(data=irmw2,mapping=aes(x=moose,y=wolves))
```
]]
.column[.content[

<img src="Lecture_Annotations_files/figure-html/irmw1_user_1_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
head(irmw2)

ggplot(data=irmw2,mapping=aes(x=moose,y=wolves)) +  
* geom_segment(mapping=aes(xend=moose.next,yend=wolves.next,color=year),
*              size=0.4,
*              arrow=arrow(length=unit(2,"mm"),angle=15,type="closed"))
```
]]
.column[.content[

<img src="Lecture_Annotations_files/figure-html/irmw1_user_2_output-1.png" width="100%" />
]]

---

```r
*p <- ggplot(data=irmw2,mapping=aes(x=moose,y=wolves)) +
* geom_segment(mapping=aes(xend=moose.next,yend=wolves.next,color=year),
*              size=0.4,
*              arrow=arrow(length=unit(2,"mm"),angle=15,type="closed"))
 
p
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irmw1a_user_1_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p <- ggplot(data=irmw2,mapping=aes(x=moose,y=wolves)) +  
  geom_segment(mapping=aes(xend=moose.next,yend=wolves.next,color=year),  
               size=0.4,  
               arrow=arrow(length=unit(2,"mm"),angle=15,type="closed")) +  
* geom_point(size=1.2) +
* labs(title="Isle Royale Wolf and Moose Abundance, 1970-1990",
*      subtitle="Parvovirus outbreak in 1980",
*      x="Moose Abundance",y="Wolf Abundance",
*      caption="Source: https://isleroyalewolf.org") +
* theme_bw() + theme(panel.grid=element_blank(),legend.position="none",
*                    aspect.ratio=1)
 
p
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irmw1a_user_2_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p <- ggplot(data=irmw2,mapping=aes(x=moose,y=wolves)) +  
  geom_segment(mapping=aes(xend=moose.next,yend=wolves.next,color=year),  
               size=0.4,  
               arrow=arrow(length=unit(2,"mm"),angle=15,type="closed")) +  
  geom_point(size=1.2) +  
  labs(title="Isle Royale Wolf and Moose Abundance, 1970-1990",  
       subtitle="Parvovirus outbreak in 1980",  
       x="Moose Abundance",y="Wolf Abundance",  
       caption="Source: https://isleroyalewolf.org") +  
  theme_bw() + theme(panel.grid=element_blank(),legend.position="none",  
                     aspect.ratio=1) +  
* geom_point(data=filter(irmw,year==1980),color="red",size=1.2)
 
p
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irmw1a_user_3_output-1.png" width="100%" />
]]

---

```r
*p 
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irmw2_auto_1_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p +  
* geom_text(mapping=aes(label=year))
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irmw2_auto_2_output-1.png" width="100%" />
]]

---

```r
p +  
  geom_text(  
    mapping=aes(label=year5),  
    )  
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irmw3_non_seq_1_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p +  
  geom_text(  
    mapping=aes(label=year5),  
*   vjust="bottom",
    )  
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irmw3_non_seq_2_output-1.png" width="100%" />
]]
---
class: split-50
count: false

```r
p +  
  geom_text(  
    mapping=aes(label=year5),  
    vjust="bottom",  
*   nudge_y=1
    )  
```
]]
.column[.content[
<img src="Lecture_Annotations_files/figure-html/irmw3_non_seq_3_output-1.png" width="100%" />
]]

---

# Next Time

<font size="7">We will show how to efficiently create separate panels for plots with subgroups.</font>