Microbes on Earth - ES2304 & ES7027

layout: true
background-image: url(img/logo-course-microbe.jpg), url(img/logo_SBR.png), url(img//NTU-Logo-full-colour.png)
background-position: right 10px top 20px,  right 50px bottom 50px,left 50px bottom 50px, top 350px left 500px 
background-size: 35%, 25%, 20%

# Microbes on Earth

---

## R session 03 - Data viz

.font120[**Daniel Vaulot**]

2021-10-12

---
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class: middle, inverse

# Outline

.font150[
* Graph types
* Grammar of graphics
* Playing with ggplot2
* Multiple graphs
* ggplot2 syntax
]

---
layout: false
# Installation and Resources

.pull-left[
## Packages

* ggplot2
* patchwork

## Download

* R-session-03.zip

## Reading assignement
* [Chapter 28 of R for data science](https://r4ds.had.co.nz/graphics-for-communication.html)

## Resources
* [Fundamental of data visualization](https://serialmentor.com/dataviz/)
* [Data visualization: practical introduction](http://socviz.co/lookatdata.html#what-makes-bad-figures-bad)
]

.pull-right[

<img src="img/R_for_datascience.png" width="60%" style="display: block; margin: auto;" />
]

---

# Data vizualization

<img src="img/tidy_worflow.png" width="55%" style="display: block; margin: auto;" />
--

## Graph purposes

.pull-left[
* **Analysis graphs**
    * design to see patterns, trends
    * aid the process of data description
    * interpretation]
--
.pull-right[
* **Presentation graphs**
    * design to attract attention
    * make a point
    * illustrate a conclusion
]

.font70[Source: Michael Friendly - http://datavis.ca/courses/RGraphics/]

---
layout: true

# Graph types

---

.left-column[
## Jitter
* Two variables numerical
]
--

.right-column[
<img src="img/graph_jitter.png" width="90%" style="display: block; margin: auto;" />
]

---

.left-column[
## Bubble
* Two variables numerical
* **Add another variable numerical**
]

.right-column[
<img src="img/graph_bubble.png" width="90%" style="display: block; margin: auto;" />
]

---
exclude: true

.left-column[
## Animate

* Two variables numerical
* One variable numerical
* One variable categorical
* **Animate another variable**
]

.right-column[
<img src="img/graph_animate.gif" width="60%" style="display: block; margin: auto;" />
]

---
exclude: true 
## Times series

.left-column[
* Line graph
]
.right-column[
<img src="img/graph_time_series.png" width="90%" style="display: block; margin: auto;" />
]

---
## Bargraphs

.left-column[
* One variable categorical
* One variable numerical
]
.right-column[
<img src="img/graph_bars2.png" width="90%" style="display: block; margin: auto;" />
]

---
## Bargraphs

.left-column[
* Rotate
]
.right-column[
<img src="img/graph_bars1.png" width="90%" style="display: block; margin: auto;" />
]

---
## Bargraphs

.left-column[
* Two variable categorical
* One variable numerical
]

.right-column[
<img src="img/graph_bars3.png" width="90%" style="display: block; margin: auto;" />
]

---
## Boxplots

.left-column[
* One variable categorical
* One variable numerical but with many values
]

.right-column[
<img src="img/graph_box.png" width="70%" style="display: block; margin: auto;" />
]

---
## Treemaps

.left-column[
* One variable categorical
* One variable numerical
* Much better than pie charts
]

.right-column[
<img src="img/graph_treemap.png" width="60%" style="display: block; margin: auto;" />
]

---
exclude: true

## 3D

.left-column[
* Three variable numerical
* Avoid unless it is a simple shape
]

.right-column[
<img src="img/graph_3d.png" width="70%" style="display: block; margin: auto;" />
]

---
exclude: true

## Contours

.left-column[
* Three variable numerical
* Better than 3D
]

.right-column[
<img src="img/graph_contour.png" width="60%" style="display: block; margin: auto;" />
]

---
background-image: url(img/graph_gallery.png)
background-position: right 20px top 20px
background-size: 60%

## Many...

.left-column[
* Choose as a function of what you want to analyze or the story you want to tell
* https://www.r-graph-gallery.com/all-graphs/
]

---
exclude: true 
layout: false

background-image: url(img/wooclap_01.png)
background-position: middle center 
background-size: 100%

# Wooclap - Quizz on Data wrangling

.font150[

https://www.wooclap.com/R01
]

---
layout: false

# ggplot2

@allison_horst

---
layout: true
# Initialize

---

## Load necessary libraries

```r
library("readxl") # Import the data from Excel file

library("dplyr")  # filter and reformat data frames

library("ggplot2") # graphics
```

---

## Read the data

```r
samples <- readxl::read_excel("data/CARBOM data.xlsx", 
                         sheet = "Samples_boat") %>% 
           tidyr::fill(station)
```

<table class="table table-striped table-hover table-condensed" style="font-size: 9px; margin-left: auto; margin-right: auto;">
 <thead>
  <tr>
   <th style="text-align:left;"> sample number </th>
   <th style="text-align:right;"> transect </th>
   <th style="text-align:left;"> station </th>
   <th style="text-align:left;"> date </th>
   <th style="text-align:left;"> time </th>
   <th style="text-align:right;"> depth </th>
   <th style="text-align:left;"> level </th>
   <th style="text-align:right;"> latitude </th>
   <th style="text-align:right;"> longitude </th>
   <th style="text-align:right;"> picoeuks </th>
   <th style="text-align:right;"> nanoeuks </th>
   <th style="text-align:right;"> phosphates </th>
   <th style="text-align:right;"> nitrates </th>
   <th style="text-align:right;"> temperature </th>
   <th style="text-align:right;"> salinity </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> 10 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:left;"> 81 </td>
   <td style="text-align:left;"> 2013-11-13 </td>
   <td style="text-align:left;"> 1899-12-31 01:00:00 </td>
   <td style="text-align:right;"> 140 </td>
   <td style="text-align:left;"> Deep </td>
   <td style="text-align:right;"> -27.42 </td>
   <td style="text-align:right;"> -44.72 </td>
   <td style="text-align:right;"> 3278 </td>
   <td style="text-align:right;"> 1232 </td>
   <td style="text-align:right;"> 0.20 </td>
   <td style="text-align:right;"> 0.26 </td>
   <td style="text-align:right;"> 17.3 </td>
   <td style="text-align:right;"> 35.9 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 11 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:left;"> 85 </td>
   <td style="text-align:left;"> 2013-11-13 </td>
   <td style="text-align:left;"> 1899-12-31 13:30:00 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:left;"> Deep </td>
   <td style="text-align:right;"> -26.80 </td>
   <td style="text-align:right;"> -45.30 </td>
   <td style="text-align:right;"> 16312 </td>
   <td style="text-align:right;"> 1615 </td>
   <td style="text-align:right;"> 0.29 </td>
   <td style="text-align:right;"> 0.22 </td>
   <td style="text-align:right;"> 21.3 </td>
   <td style="text-align:right;"> 36.5 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 120 </td>
   <td style="text-align:right;"> 2 </td>
   <td style="text-align:left;"> 96 </td>
   <td style="text-align:left;"> 2013-11-18 </td>
   <td style="text-align:left;"> 1899-12-31 23:50:00 </td>
   <td style="text-align:right;"> 5 </td>
   <td style="text-align:left;"> Surf </td>
   <td style="text-align:right;"> -27.39 </td>
   <td style="text-align:right;"> -47.82 </td>
   <td style="text-align:right;"> 1150 </td>
   <td style="text-align:right;"> 75 </td>
   <td style="text-align:right;"> 0.43 </td>
   <td style="text-align:right;"> 0.19 </td>
   <td style="text-align:right;"> 23.1 </td>
   <td style="text-align:right;"> 33.5 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 121 </td>
   <td style="text-align:right;"> 2 </td>
   <td style="text-align:left;"> 96 </td>
   <td style="text-align:left;"> 2013-11-18 </td>
   <td style="text-align:left;"> 1899-12-31 23:50:00 </td>
   <td style="text-align:right;"> 30 </td>
   <td style="text-align:left;"> Deep </td>
   <td style="text-align:right;"> -27.39 </td>
   <td style="text-align:right;"> -47.82 </td>
   <td style="text-align:right;"> 1737 </td>
   <td style="text-align:right;"> 218 </td>
   <td style="text-align:right;"> 0.43 </td>
   <td style="text-align:right;"> 0.23 </td>
   <td style="text-align:right;"> 22.6 </td>
   <td style="text-align:right;"> 33.7 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 122 </td>
   <td style="text-align:right;"> 2 </td>
   <td style="text-align:left;"> 96 </td>
   <td style="text-align:left;"> 2013-11-18 </td>
   <td style="text-align:left;"> 1899-12-31 23:50:00 </td>
   <td style="text-align:right;"> 50 </td>
   <td style="text-align:left;"> Deep </td>
   <td style="text-align:right;"> -27.39 </td>
   <td style="text-align:right;"> -47.82 </td>
   <td style="text-align:right;"> 853 </td>
   <td style="text-align:right;"> 234 </td>
   <td style="text-align:right;"> 0.56 </td>
   <td style="text-align:right;"> 0.21 </td>
   <td style="text-align:right;"> 20.3 </td>
   <td style="text-align:right;"> 35.9 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 125 </td>
   <td style="text-align:right;"> 2 </td>
   <td style="text-align:left;"> 98 </td>
   <td style="text-align:left;"> 2013-11-18 </td>
   <td style="text-align:left;"> 1899-12-31 05:00:00 </td>
   <td style="text-align:right;"> 5 </td>
   <td style="text-align:left;"> Surf </td>
   <td style="text-align:right;"> -27.59 </td>
   <td style="text-align:right;"> -47.39 </td>
   <td style="text-align:right;"> 3086 </td>
   <td style="text-align:right;"> 1300 </td>
   <td style="text-align:right;"> 0.29 </td>
   <td style="text-align:right;"> 0.25 </td>
   <td style="text-align:right;"> 23.1 </td>
   <td style="text-align:right;"> 35.7 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 126 </td>
   <td style="text-align:right;"> 2 </td>
   <td style="text-align:left;"> 98 </td>
   <td style="text-align:left;"> 2013-11-18 </td>
   <td style="text-align:left;"> 1899-12-31 05:00:00 </td>
   <td style="text-align:right;"> 50 </td>
   <td style="text-align:left;"> Deep </td>
   <td style="text-align:right;"> -27.59 </td>
   <td style="text-align:right;"> -47.39 </td>
   <td style="text-align:right;"> 1217 </td>
   <td style="text-align:right;"> 782 </td>
   <td style="text-align:right;"> 0.25 </td>
   <td style="text-align:right;"> 0.20 </td>
   <td style="text-align:right;"> 23.7 </td>
   <td style="text-align:right;"> 37.2 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 127 </td>
   <td style="text-align:right;"> 2 </td>
   <td style="text-align:left;"> 98 </td>
   <td style="text-align:left;"> 2013-11-18 </td>
   <td style="text-align:left;"> 1899-12-31 05:00:00 </td>
   <td style="text-align:right;"> 85 </td>
   <td style="text-align:left;"> Deep </td>
   <td style="text-align:right;"> -27.59 </td>
   <td style="text-align:right;"> -47.39 </td>
   <td style="text-align:right;"> 3420 </td>
   <td style="text-align:right;"> 226 </td>
   <td style="text-align:right;"> 0.25 </td>
   <td style="text-align:right;"> 0.47 </td>
   <td style="text-align:right;"> 22.9 </td>
   <td style="text-align:right;"> 37.0 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 13 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:left;"> 86 </td>
   <td style="text-align:left;"> 2013-11-13 </td>
   <td style="text-align:left;"> 1899-12-31 17:00:00 </td>
   <td style="text-align:right;"> 105 </td>
   <td style="text-align:left;"> Deep </td>
   <td style="text-align:right;"> -26.33 </td>
   <td style="text-align:right;"> -45.41 </td>
   <td style="text-align:right;"> 6366 </td>
   <td style="text-align:right;"> 1007 </td>
   <td style="text-align:right;"> 0.34 </td>
   <td style="text-align:right;"> 0.15 </td>
   <td style="text-align:right;"> 20.9 </td>
   <td style="text-align:right;"> 36.3 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 140 </td>
   <td style="text-align:right;"> 2 </td>
   <td style="text-align:left;"> 101 </td>
   <td style="text-align:left;"> 2013-11-18 </td>
   <td style="text-align:left;"> 1899-12-31 12:00:00 </td>
   <td style="text-align:right;"> 5 </td>
   <td style="text-align:left;"> Surf </td>
   <td style="text-align:right;"> -27.79 </td>
   <td style="text-align:right;"> -46.96 </td>
   <td style="text-align:right;"> 500 </td>
   <td style="text-align:right;"> 366 </td>
   <td style="text-align:right;"> 0.29 </td>
   <td style="text-align:right;"> 0.14 </td>
   <td style="text-align:right;"> 23.5 </td>
   <td style="text-align:right;"> 36.5 </td>
  </tr>
</tbody>
</table>

---
layout: true
# ggplot2

---

## A simple plot

.left-code[
* Choose the data set
* Choose the geometric representation
* Choose the __aesthetics__ : x,y, color, shape etc...

```r
ggplot(data=samples) + 
geom_point(mapping = aes(x=phosphates, 
                         y=nitrates))
```

* All functions are from __ggplot2__ package unless specified
]
--
.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-19-1.png" width="70%" style="display: block; margin: auto;" />
]

---
## The grammar of graphics

Every graph can be described as a combination of independent building blocks:
* **data**: a data frame: quantitative, categorical; local or data base query
* **aes**thetic mapping of variables into visual properties: size, color, x, y
* **geom**etric objects (“geom”): points, lines, areas, arrows, …
* **coord**inate system (“coord”): Cartesian, log, polar, map

---

.left-code[
Syntax

```r
 ggplot(data=samples) + 
  geom_point(mapping = aes(x=phosphates, 
                           y=nitrates))
```
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-21-1.png" width="70%" style="display: block; margin: auto;" />
]

---

.left-code[
Alternatively

```r
 ggplot(data=samples, 
        mapping = aes(x=phosphates, 
                      y=nitrates)) + 
  geom_point()
```
* If different geometries origniate from different datasets or have different mapping the datasets or the mapping must be called **inside** the geom function.
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-22-1.png" width="70%" style="display: block; margin: auto;" />
]

---

.left-code[
Alternatively

```r
 ggplot(samples, 
        aes(x=phosphates, 
            y=nitrates)) + 
  geom_point()
```
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-23-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Make dot size bigger

.left-code[

```r
 ggplot(samples,
        aes(x=phosphates, 
            y=nitrates)) 
```
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-24-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Make dot size bigger

.left-code[

```r
 ggplot(samples,
        aes(x=phosphates, 
            y=nitrates)) + 
  geom_point(size=5)
```
* Add: __size=5__ outside of the aesthetics function
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-25-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Color according to depth level (discrete)

.left-code[

```r
 ggplot(samples,
        aes(x=phosphates, 
            y=nitrates,
            color=level)) + 
  geom_point(size=5)
```
* The mapping aesthetics must be an argument of the aes function
* geom_point(**color=level**, size=5) will generate an error...
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-26-1.png" width="70%" style="display: block; margin: auto;" />
]

---
## Color according to depth  (continuous)

.left-code[

```r
 ggplot(samples,
        aes(x=phosphates, 
            y=nitrates,
            color=depth)) + 
  geom_point(size=5)
```
* Add: __color=depth__ 
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-27-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Symbol according to transect (continuous)

.left-code[

```r
 ggplot(samples,
        aes(x=phosphates, 
            y=nitrates,
            color=depth,
            shape=transect)) + 
  geom_point(size=5)
```
* Add: __shape=transect__ 
]

.right-plot[

```
Error: A continuous variable can not be mapped to shape
```

<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-28-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Symbol according to transect (continuous)

.left-code[

```r
 ggplot(samples,
        aes(x=phosphates, 
            y=nitrates,
            color=depth,
            shape=as.character(transect))) + 
  geom_point(size=5)
```
* Add: __shape=as.character(transect)__ 
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-29-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Panels depending on one variable

.left-code[

```r
 ggplot(samples,
        aes(x=phosphates, 
            y=nitrates)) +
  geom_point() +
  facet_wrap(~ level) 
```
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-30-1.png" width="70%" style="display: block; margin: auto;" />
]

---
## Adding a regression line

.left-code[

```r
 ggplot(samples,
        aes(x=phosphates, 
            y=nitrates, 
            color=level)) +
  geom_point(size=5) +
  geom_smooth(mapping = aes(x=phosphates, 
                            y=nitrates), 
              method="lm")
```
* Add: __geom_smooth()__
* You can choose the type of smoothing "lm" is for linear model
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-31-1.png" width="70%" style="display: block; margin: auto;" />
]

---
## Adding a regression line

.left-code[

```r
 ggplot(samples,
        aes(x=phosphates, 
            y=nitrates)) +
  geom_point(aes(color=level), 
             size=5) +
  geom_smooth(mapping = aes(x=phosphates, 
                            y=nitrates), 
              method="lm")
```
* If the mapping is in the ggplot function is for all the geom....
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-32-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Finalizing the graph

.left-code[

```r
 ggplot(samples) + 
  geom_point(mapping = aes(x=phosphates, 
                           y=nitrates,
                           color=level), 
             size=5) +
  geom_smooth(mapping = aes(x=phosphates, 
                            y=nitrates), 
              method="lm") +
  xlab("Phosphates") + 
  ylab("Nitrates") + 
  ggtitle("CARBOM cruise")
```
* Add: __geom_smooth()__
* You can choose the type of smoothing "lm" is for linear model
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-33-1.png" width="70%" style="display: block; margin: auto;" />
]

---

layout: true

# Putting several graphs together

---
exclude: true 
## First graph

.left-code[

```r
 g1 <- ggplot(samples) + 
  geom_point(mapping = aes(x=phosphates, 
                           y=nitrates,color=
                             level), size=5) +
  geom_smooth(mapping = aes(x=phosphates, 
                            y=nitrates), 
              method="lm") +
  xlab("Phosphates") + 
  ylab("Nitrates")

g1
```

]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-34-1.png" width="70%" style="display: block; margin: auto;" />
]

---
exclude: true 
## Second graph

.left-code[

```r
 g2<- ggplot(samples) + 
  geom_point(mapping = aes(x=nanoeuks, 
                           y=picoeuks,
                           color=level), 
             size=5) +
  geom_smooth(mapping = aes(nanoeuks, 
                            y=picoeuks), 
              method="lm") +
  xlab("Pico-eukaryotes") + 
  ylab("Nano-eukaryotes")

g2
```

]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-35-1.png" width="70%" style="display: block; margin: auto;" />
]

---
exclude: true 
## Package patchwork

* https://patchwork.data-imaginist.com/index.html

.left-code[

```r
library(patchwork)
(g1 + g2)/g1
```
See also packages : 
* `gridExtra`
* `cowplot`
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-36-1.png" width="70%" style="display: block; margin: auto;" />
]

---
exclude: true

## Package patchwork

.left-code[
* Adding annotation
* Collecting legends

```r
g1 / g2 +
  plot_annotation(tag_levels = 'A') +
  plot_layout(guides = 'collect')
```
]

.right-plot[
<img src="R-session-03-data_visualization_files/figure-html/unnamed-chunk-37-1.png" width="70%" style="display: block; margin: auto;" />
]

---
layout: true

# ggplot2 syntax

---
## Anatomy of a plot

---

## Geometries

---
## Continuous x and y

---

## Plotting error

---

## Discrete x - Continuous y

---

## Continuous x

---
exclude: true 
## 3D

---

## Modifying axis and scales

---
background-image: url(img/color_palettes.png)
background-position: right 20px bottom 150px
background-size: 60%

## Palettes

.pull-left[
* Package tmaptools : https://github.com/mtennekes/tmaptools
    * Function : `palette_explorer()`

* Package paletteer : https://github.com/EmilHvitfeldt/paletteer
    * More than 1000 palettes
]

---
background-image: url(img/color_palette_viridis.png)
background-position: right 20px top 100px
background-size: 60%

## Palettes
    
* Use color blind friendly palettes
    * viridis (e.g. scale_colour_viridis_c)

---
exclude: true 
## Themes

---
exclude: true 
layout: false

# Extensions

---
layout: false
class: inverse

# Recap

.font150[
- Conceptualize your graph before coding
]
--

.font150[
- Decide what element is fixed and what varies
]

--
.font150[
- It takes time to get what you want...
]

--
.font150[
- Exploratory vs. final
]

---
exclude: true 
layout: true

# Next time: Create maps

.pull-left[

## What you will learn :
* Create simple maps
* Create interactive maps
* Create thematic maps

## Install
* rworldmap
* leaflet
* sf
* raster
* spData
* tmap
* ggplot2

]

.pull-right[

## Reading list
* [Geocomputation with R](https://geocompr.robinlovelace.net/)

]