Plot a lot with ggplot2 to find plots

# Plot a lot with ggplot2 to find plots
## R-Ladies Colombo Meetup
### Priyanga Dilini Talagala
### 2021/01/27

---

background-image:url('fig/tidyworkflow1.png')
background-position: 60% 80%
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class: top, center
# Tidy Workflow
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background-image:url('fig/tidyworkflow2.png')
background-position: 60% 80%
background-size: 100%
class: top, center
# Tidy Workflow
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background-image:url('fig/tidyworkflow3.png')
background-position: 60% 80%
background-size: 100%
class: top, center
# Tidy Workflow
---
class: inverse

## The Datasaurus Dozen

```r
library(datasauRus)
library(ggplot2)
library(gganimate)

ggplot(datasaurus_dozen, aes(x=x, y=y))+
  geom_point()+
  theme_minimal() +
  transition_states(dataset, 3, 1) + 
  theme(aspect.ratio = 1)
```

---

## The Datasaurus Dozen

```r
library(datasauRus)
library(ggplot2)
library(gganimate)

ggplot(datasaurus_dozen, aes(x=x, y=y))+
  geom_point()+
  theme_minimal() +
  transition_states(dataset, 3, 1) + 
  theme(aspect.ratio = 1)
```

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<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-3-1.gif" style="display: block; margin: auto;" />
]
.pull-right[

Summary statistics | 
-------------------|----
X Mean     | 54.26
Y Mean     | 47.83
X SD    | 16.77
Y SD     | 26.94
Corr.    |  -0.06

]

---

# The Grammar of Graphics

---

### The Book
# The Grammar of Graphics

---

#### R Base Graphics

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<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-6-1.png" style="display: block; margin: auto;" />

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class: middle, center
## The Grammar of Graphics

.pull-left[
Pie Chart
<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-10-1.png" style="display: block; margin: auto;" />

Line Chart
<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-11-1.png" style="display: block; margin: auto;" />

]
.pull-right[

Bar Chart
<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-12-1.png" style="display: block; margin: auto;" />

Scatterplot
<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-13-1.png" style="display: block; margin: auto;" />
]
].pull-right[

<img src="fig/7_GG_a.png" width="1223" height="100%" style="display: block; margin: auto;" />
]

---
## The Grammar of Graphics

Size measurements for adult foraging penguins near Palmer Station, Antarctica

```
Rows: 344
Columns: 8
$ species <fct> Adelie, Adelie, Adelie, Adelie, Adelie, Adelie, Ade…
$ island <fct> Torgersen, Torgersen, Torgersen, Torgersen, Torgers…
$ bill_length_mm <dbl> 39.1, 39.5, 40.3, NA, 36.7, 39.3, 38.9, 39.2, 34.1,…
$ bill_depth_mm <dbl> 18.7, 17.4, 18.0, NA, 19.3, 20.6, 17.8, 19.6, 18.1,…
$ flipper_length_mm <int> 181, 186, 195, NA, 193, 190, 181, 195, 193, 190, 18…
$ body_mass_g <int> 3750, 3800, 3250, NA, 3450, 3650, 3625, 4675, 3475,…
$ sex <fct> male, female, female, NA, female, male, female, mal…
$ year <int> 2007, 2007, 2007, 2007, 2007, 2007, 2007, 2007, 200…
```

<img src="fig/15_palmerpenguins.png" width="35%" style="display: block; margin: auto;" />
].pull-right[

<img src="fig/8_GG_1.png" width="100%" style="display: block; margin: auto;" />
]
---

## The Grammar of Graphics
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<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-18-1.png" style="display: block; margin: auto;" />
].pull-right[

<img src="fig/9_GG_2.png" width="100%" style="display: block; margin: auto;" />
]
---

## The Grammar of Graphics
.pull-left[

**Counts**

```
# A tibble: 3 x 2
 species n
 <fct> <int>
1 Adelie 152
2 Chinstrap 68
3 Gentoo 124
```
].pull-right[

<img src="fig/10_GG_3.png" width="100%" style="display: block; margin: auto;" />
]
---

## The Grammar of Graphics
.pull-left[
<img src="fig/16_scale.png" width="100%" style="display: block; margin: auto;" />
].pull-right[

<img src="fig/11_GG_4.png" width="100%" style="display: block; margin: auto;" />
]
---

## The Grammar of Graphics
.pull-left[

**Bar Plot**

].pull-right[

<img src="fig/12_GG_5.png" width="100%" style="display: block; margin: auto;" />
]

---

## The Grammar of Graphics
.pull-left[

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-29-1.png" style="display: block; margin: auto;" />
].pull-right[

<img src="fig/13_GG_6.png" width="100%" style="display: block; margin: auto;" />
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---

## The Grammar of Graphics
.pull-left[
<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-31-1.png" style="display: block; margin: auto;" />

].pull-right[

<img src="fig/14_GG_7.png" width="100%" style="display: block; margin: auto;" />
]
---

## The Grammar of Graphics
.pull-left[
<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-33-1.png" style="display: block; margin: auto;" />

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-34-1.png" style="display: block; margin: auto;" />
].pull-right[

<img src="fig/14_GG_7.png" width="100%" style="display: block; margin: auto;" />
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---

## The Grammar of Graphics
.pull-left[
<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-36-1.png" style="display: block; margin: auto;" />

**Excel Theme**

].pull-right[

<img src="fig/7_GG.png" width="100%" style="display: block; margin: auto;" />
]
---

# The ggplot2 API

<img src="fig/ggplot.png" width="40%" style="display: block; margin: auto;" />
---

## Which dataset to plot?

---

The Palmer Archipelago penguins. Artwork by `@allison_horst`.

<img src="fig/18_culmen_depth.png" width="70%" style="display: block; margin: auto;" />
].pull-right[

```
# A tibble: 6 x 8
 species island bill_length_mm bill_depth_mm flipper_length_… body_mass_g sex 
 <fct> <fct> <dbl> <dbl> <int> <int> <fct>
1 Adelie Torge… 39.1 18.7 181 3750 male 
2 Adelie Torge… 39.5 17.4 186 3800 fema…
3 Adelie Torge… 40.3 18 195 3250 fema…
4 Adelie Torge… NA NA NA NA <NA> 
5 Adelie Torge… 36.7 19.3 193 3450 fema…
6 Adelie Torge… 39.3 20.6 190 3650 male 
# … with 1 more variable: year <int>
```

---
## Which dataset to plot?

```r
ggplot() 
```

---
## Which dataset to plot?

```r
*ggplot(data = penguins)
```

---

## Mapping

---
## Which columns to use for x and y?

```r
ggplot(data = penguins,
*      mapping = aes(x = flipper_length_mm,
*                    y = body_mass_g))
```

---
class: middle, center

## Geometries

---
## How to draw the plot?

```r
ggplot(data = penguins,
       mapping = aes(x = flipper_length_mm,
                     y = body_mass_g)) +
* geom_point()
```

---

## Data, Mapping and Geometries

<img src="fig/20_maingg.png" width="40%" style="display: block; margin: auto;" />
---
## How to draw the plot?

```r
ggplot(data = penguins) +
* geom_point(mapping = aes(x = flipper_length_mm,
*                          y = body_mass_g))
```

---

## How to draw the plot?

```r
ggplot() +
  geom_point(mapping = aes(x = flipper_length_mm, 
                           y = body_mass_g),
*            data = penguins)
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-59-1.png" style="display: block; margin: auto;" />
---

## Mapping Colours

```r
ggplot(penguins) +
  geom_point( aes(x = flipper_length_mm,
                  y = body_mass_g,
*                 color = species,
*                 shape = species))
```

---
## Mapping Colours

```r
ggplot(penguins) +
 geom_point( aes(x = flipper_length_mm,
 y = body_mass_g,
* colour = flipper_length_mm < 205))
```

---
## Setting Colours

```r
ggplot(penguins) +
  geom_point( aes(x = flipper_length_mm,
                  y = body_mass_g),
*                 colour = 'purple')
```

---

```r
ggplot(penguins, 
       aes(x = flipper_length_mm,
           y = body_mass_g,
           color = species, 
           shape = species)) +
  geom_point() +
* geom_density_2d()
```

- Syntax starts with `geom_*`.
- eg: geom_histogram(), geom_bar(), geom_boxplot().
- Each shape has its own specific aesthetics arguments.

].pull-right[
<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-67-1.png" style="display: block; margin: auto;" />

]
--

```r
ggplot(penguins) +
  geom_histogram(
*   aes(x = flipper_length_mm))
```
].pull-right[

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-69-1.png" style="display: block; margin: auto;" />
]
---

Each shape has its own specific aesthetics arguments.

`?geom_point`

---
class: middle, center

## Statistics

---
## `geom_bar()` uses `stat_count()` by default

```r
ggplot(penguins) +
  geom_bar(aes(x = species)) 
```

---
## `after_stat()`

```r
ggplot(penguins) +
  geom_bar(aes(x = species,
*              y = after_stat(100*count/ sum  (count)) ))
```

---

## Old version of ggplot2

```r
ggplot(penguins) +
  geom_bar(aes(x = species,
*              y = 100*(..count..)/sum(..count..) ))
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-77-1.png" style="display: block; margin: auto;" />
---
## `after_stat()` (ggplot2 3.0.0)

```r
ggplot(penguins) +
  geom_bar(aes(x = species,
*              y = after_stat(100*count/ sum  (count)) ))
```

---
- There are two ways to use statistical functions.

```r
ggplot(penguins,
       aes(x = flipper_length_mm,
           y = body_mass_g)) +
* stat_summary(
*   geom ="point",
    fun.y ="mean",
    colour ="red")
```

].pull-right[
**define `geom_*()` function and `stat` argument inside that function**

```r
ggplot(penguins,
       aes(x = flipper_length_mm,
           y = body_mass_g)) +
* geom_point(
*   stat ="summary",
    fun.y ="mean",
    colour ="red")
```

]

---

Statistics  | Geometries
------------|----------
`stat_count` | `geom_bar`
`stat_boxplot` | `geom_boxplot`
`stat_identity` | `geom_col`
`stat_bin`  | `geom_bar`, `geom_histogram`
`stat_density` | `geom_density`

<div class="figure" style="text-align: center">
<img src="fig/23_help.png" alt="?geom_boxplot" width="100%" />
?geom_boxplot
</div>
].pull-right[

<div class="figure" style="text-align: center">
<img src="fig/24_help.png" alt="?geom_bar" width="120%" />
?geom_bar
</div>
]
---
class: middle, center

## Scales

<img src="fig/25_scale.png" width="40%" style="display: block; margin: auto;" />
---

## Scales

```r
ggplot(penguins) +
  geom_point( aes(x = flipper_length_mm,
                  y = body_mass_g,
*                 color = species,
*                 shape = species))
```

---

## Scales

```r
ggplot(penguins) +
  geom_point( aes(x = flipper_length_mm,
                  y = body_mass_g,
*                 color = species,
*                 shape = island))
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-88-1.png" style="display: block; margin: auto;" />
---

## Scales

```r
ggplot(penguins) +
  geom_point( aes(x = flipper_length_mm,
                  y = body_mass_g,
*                 color = bill_length_mm,
*                 shape = island))
```

---

## Scales

```r
ggplot(penguins) +
  geom_point(aes(x = flipper_length_mm,
                  y = body_mass_g,
                  color = species)) +
* scale_color_brewer(type = 'qual',
*                    palette =  'Dark2')
```

- `scale_<aesthetic>_<type>`

---

`RColorBrewer::display.brewer.all()`

---

```r
ggplot(penguins) +
  geom_point(aes(x = flipper_length_mm,
                 y = body_mass_g,
*                color = species)) +
* scale_color_viridis_d()
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-95-1.png" style="display: block; margin: auto;" />
--

- `viridis` and `RColorBrewer` provide different color scales that are robust to color-blindness.
--

- For details and an interactive palette selection tools see http://colorbrewer.org

---

```r
ggplot(penguins) +
  geom_point(aes(x = flipper_length_mm,
                 y = body_mass_g,
                 color = species,
                 shape = species,
                 alpha = species)) +
* scale_x_continuous( breaks = c(170,200,230)) +
* scale_y_log10() +
* scale_colour_viridis_d(direction = -1, option= 'plasma') +
* scale_shape_manual( values = c(17,18,19)) +
* scale_alpha_manual( values = c( "Adelie" = 0.6, "Gentoo" = 0.5, #
*                                 "Chinstrap" = 0.7))
```

---
class: middle, center

## Facets

<img src="fig/28_facets.png" width="40%" style="display: block; margin: auto;" />
---
## `facet_wrap()`

```r
ggplot(penguins) +
  geom_point(aes(
    x = flipper_length_mm,
    y = body_mass_g)) + 
* facet_wrap(vars(species))
```

---
## `facet_wrap()`

```r
ggplot(penguins) +
  geom_point(aes(
    x = flipper_length_mm,
    y = body_mass_g)) + 
  facet_wrap(vars(species),
*            scales = "free_x")
```

---

## `facet_grid()`

```r
ggplot(penguins) +
  geom_point(aes(
    x = flipper_length_mm,
    y = body_mass_g)) + 
* facet_grid( vars(species), vars(sex))
```

---
class: middle, center

## Coordinates

---
## Coordinates

```r
ggplot(penguins) +
  geom_bar(aes(x= species, fill = species)) 
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-107-1.png" style="display: block; margin: auto;" />
---

```r
ggplot(penguins) +
  geom_bar(aes(x= species, fill = species)) +
* coord_flip()
```

- There are two types of coordinate systems:  
   - Linear coordinate systems
   - Non-linear coordinate systems 
--

- Linear coordinate systems : `coord_cartesian()`, `coord_flip()`, `coord_fixed()`
--

- Non-linear coordinate systems : eg : `coord_map()`, `coord_quickmap()`, `coord_sf()`, `coord_polar()`, `coord_trans()`
---

## Coordinates

```r
ggplot(penguins) +
  geom_bar(aes(x= species, fill = species)) +
* coord_polar()
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-111-1.png" style="display: block; margin: auto;" />
---

## Coordinates

```r
ggplot(penguins) +
  geom_bar(aes(x= species, fill = species)) +
* coord_polar(theta = "y")
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-113-1.png" style="display: block; margin: auto;" />
---
#### Zooming into a plot

```r
ggplot(penguins) +
  geom_bar(aes(x= year, fill = species))
```

---

#### Zooming into a plot with `scale`

```r
ggplot(penguins) +
  geom_bar(aes(x= year, fill = species)) +
* scale_y_continuous(limits = c(0,115))
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-117-1.png" style="display: block; margin: auto;" />
--

**When zooming with `scale`, any data outside the limits is thrown away**

---

#### Proper zoom with `coord_cartesian()`

```r
ggplot(penguins) +
  geom_bar(aes(x= year, fill = species)) +
* coord_cartesian(ylim = c(0,115))
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-120-1.png" style="display: block; margin: auto;" />
--

**Zooming with `coord` is like looking at the plot under a magnifying glass.**

---
class: middle, center

## Themes

<img src="fig/32_themes.png" width="40%" style="display: block; margin: auto;" />
---
These are complete themes which control all **non-data** display.

```r
ggplot(data = penguins,
       aes(x = flipper_length_mm,
           y = body_mass_g)) +
  geom_point(aes(
    color = species,
    shape = species),
    size = 3,
    alpha = 0.8) +
* theme_minimal()
```

].pull-right[

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-124-1.png" style="display: block; margin: auto;" />
]

--
.pull-left[

```r
ggplot(data = penguins,
 aes(x = flipper_length_mm,
 y = body_mass_g)) +
 geom_point(aes(
 color = species,
 shape = species),
 size = 3,
 alpha = 0.8) +
* theme_dark()
```
].pull-right[
<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-126-1.png" style="display: block; margin: auto;" />
]

---
Create custom themes in ggplot.

```r
ggplot(penguins,
       aes(x = flipper_length_mm,
           y = body_mass_g)) +
  geom_point(aes(color = species,
                 shape = species),
             size = 3, alpha = 0.8) +
  scale_color_viridis_d() +
* theme_minimal() +
* labs(
*   title = "Penguin size, Palmer Station LTER",
*   subtitle = "Flipper length and body mass for Adelie, Chinstrap and Gentoo Penguins",
*   x = "Flipper length (mm)",
*   y = "Body mass (g)",
*   color = "Penguin species",
*   shape = "Penguin species") +
* theme(
*   aspect.ratio = 1,
*   legend.position = c(0.2, 0.7),
*   legend.background =
*     element_rect(
*       fill = "white",
*       color = NA),
*   plot.title.position = "plot",
*   plot.caption =
*     element_text(
*       hjust = 0,
*       face= "italic"),
*   plot.caption.position = "plot")
```

].pull-right[

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-129-1.png" style="display: block; margin: auto;" />
]

---

background-image:url('fig/33_gg.png')
background-position: 50% 50%
background-size: 100%
class: top, center
---
class: inverse, middle, center

# ggplot2 extensions
---
background-image:url('fig/34_extension.png')
background-position: 50% 90%
background-size: 100%
class: top, center
### ggplot2 extensions: `https://exts.ggplot2.tidyverse.org/`

---

# 1. `patchwork` for plot composition

<img src="fig/35_patchwork.png" width="40%" style="display: block; margin: auto;" />
---

```r
p1 <- ggplot(data = penguins, aes(x = flipper_length_mm, y = body_mass_g)) +
 geom_point(aes(color = species, shape = species), size = 2) +
 scale_color_manual(values = c("darkorange","darkorchid","cyan4")) +
 theme(aspect.ratio = 1)

p2 <- ggplot(data = penguins, aes(x = bill_length_mm, y = bill_depth_mm)) +
 geom_point(aes(color = species, shape = species), size = 2) +
 scale_color_manual(values = c("darkorange","darkorchid","cyan4")) +
 theme(aspect.ratio = 1)

p3 <- ggplot(data = penguins, aes(x = flipper_length_mm)) +
 geom_histogram(aes(fill = species), alpha = 0.5, position = "identity") +
 scale_fill_manual(values = c("darkorange","darkorchid","cyan4"))
```

---

```r
library(patchwork)
p1 + p3 
```

---

```r
library(patchwork)
(p1 | p2) / p3
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-133-1.png" style="display: block; margin: auto;" />
---

```r
library(patchwork)
p <- (p1 | p2) / p3

*p + plot_layout(guide = 'collect')
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-134-1.png" style="display: block; margin: auto;" />
---

```r
library(patchwork)
p <- (p1 | p2) / p3

p +
  plot_layout(guide = 'collect') +
  plot_annotation(
*   title = 'Size measurements for adult foraging penguins near Palmer Station, Antarctica',
*   tag_levels = 'A')
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-135-1.png" style="display: block; margin: auto;" />
---

```r
library(patchwork)
p <- (p1 | p2) / p3

p & 
* theme(legend.position =  'none')
```

---

# 2. `plotly`

An R package for creating **interactive web graphics** via the open source JavaScript graphing library plotly.js.

---

```r
p1 ## a ggplot object
```

---

```r
plotly::ggplotly(p1)
```

<div id="htmlwidget-9ab027e3a695639b913e" style="width:100%;height:504px;" class="plotly html-widget"></div>
<script type="application/json" 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---
class:  middle, center

# 3. `GGally`

---

```r
GGally::ggpairs(penguins[, 1:5], aes(color = species, fill = species))+
  scale_color_viridis_d() +
  scale_fill_viridis_d()
```

---
class:  middle, center

# 4. `gganimate`

<img src="fig/36_gganimate.png" width="40%" style="display: block; margin: auto;" />
---

```r
library("ggplot2")
library("dlstats")

data <- cran_stats("ggplot2")

p <- ggplot(data, aes(x= end, y = downloads)) +
 geom_line() +
 labs(title = "Download stats of ggplot2 package", x = "Time", y = "Downloads")

p
```

---

```r
library(gganimate)
p + 
* transition_reveal(along = end)
```

---

```r
p <- ggplot(penguins, aes(flipper_length_mm, body_mass_g , color = species)) +
 geom_point() + scale_color_viridis_d() +
 labs(title = "Measurements of penguins {closest_state}")+
* transition_states(states = year) + enter_grow() + exit_fade()
p
```

![](fig/39_gganim.gif)

---

# 5. `ggrepel`

<img src="fig/37_ggrepel.png" width="40%" style="display: block; margin: auto;" />
---
### Text annotation

```r
df <- penguins %>%
 filter( flipper_length_mm > 225 )

ggplot(penguins, aes(x=flipper_length_mm, y= body_mass_g))+
  geom_point()+
  theme(aspect.ratio = 1) + 
* geom_text(data= df,
*           aes(x=flipper_length_mm, y= body_mass_g, label= island))
```

<img src="RLadies-ggplot2_files/figure-html/unnamed-chunk-145-1.png" style="display: block; margin: auto;" />
---

### Text annotation

```r
ggplot(penguins, aes(x=flipper_length_mm, y= body_mass_g))+
  geom_point()+
  theme(aspect.ratio = 1) + 
* ggrepel::geom_text_repel(data= df,
*           aes(x=flipper_length_mm, y= body_mass_g, label= island))
```

---
class:  middle, center

# 6. `ggforce`

<img src="fig/38_ggforce.jpeg" width="40%" style="display: block; margin: auto;" />
---

```r
library(ggforce)

penguins <- penguins %>% drop_na()
p <- ggplot(penguins, aes(x=flipper_length_mm, y= body_mass_g))+
* geom_mark_ellipse(aes(
* filter = species == "Gentoo",
* label = 'Gentoo penguins'),
* description = 'Palmer Station Antarctica LTER and K. Gorman. 2020.') +
 geom_point()

p
```

---

```r
library(ggforce)
ggplot(penguins, aes(x=flipper_length_mm, y= body_mass_g, color = species)) +
    geom_point() +
  scale_color_viridis_d() +
    facet_zoom(x = species == "Gentoo") 
```

---

# Thank you

Slides available at:

prital.netlify.app

pridiltal

# Acknowledgements:

Hadley Wickham, Thomas Lin Pedersen and ggplot2 development team

## Key References

- ggplot2: Elegant Graphics for Data Analysis https://ggplot2-book.org/
- ggplot2 workshop by Thomas Lin Pedersen https://www.youtube.com/watch?v=h29g21z0a68

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.