Experimental design

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# Experimental Design and Analysis

---

## R session 02 - Data viz

2020-01-23

<br>
<br>
<br>
.pull-left[
<img src="img/NTU-Logo-full-colour.png" width="50%" style="display: block; margin: auto auto auto 0;" />
]

.pull-right[
<img src="img/logo_SBR.png" width="50%" style="display: block; margin: auto 0 auto auto;" />
]

---

## Outline

.font150[
* Tidy data
* Graph types
* Grammar of graphics
* Read the data
* Playing with ggplot2
* ggplot2 syntax
* Your turn
]

---
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# Installation and Resources

.pull-left[
## Packages
* readxl  : Reading Excel files
* readr   : Reading and writing Text files
* dplyr : Filter and reformat data frames
* ggplot2 :plotting

## Download

* R-session-03.zip

## Resources
* [Chapter 5 and 28 of R for data science](https://r4ds.had.co.nz/graphics-for-communication.html)
* [Fundamental of data visualization](https://serialmentor.com/dataviz/)
* [Data visualization: practical introduction](http://socviz.co/lookatdata.html#what-makes-bad-figures-bad)
]

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

---

# Tidy data

1. Each variable must have its own column.
2. Each observation must have its own row.
2. Each value must have its own cell.

---
# Tidy workflow

<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
]

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# Graph types

---

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

---

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

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.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;" />
]

---
## 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

---
## Boxplots

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## Treemaps

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

---

## 3D

---

## Contours

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

---
.left-column[
## Many...
]

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

* 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/

---
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# Initialize

## Load necessary libraries

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

library("ggplot2") # graphics
```

---
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# Reading the data

---

## CARBOM cruise off Brazil

]

* Stations
* Depth
* Coordinates
* Temperature, Salinity
* Nitrates, Phosphates

]

---

## Microbial populations

.pull-right[
<img src="img/carbom_flow_cytometry.png" width="80%" style="display: block; margin: auto;" />
]
* Flow cytometry : 
    * pico-eukaryotes
    * nano-eukaryotes

---

## Text file - TAB delimited

---

## Reading a text file

```r
  samples <- readr::read_tsv("data/CARBOM data.txt")
```

<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;"> 13/11/2013 </td>
   <td style="text-align:left;"> 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;"> 13/11/2013 </td>
   <td style="text-align:left;"> 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;"> 18/11/2013 </td>
   <td style="text-align:left;"> 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;"> 18/11/2013 </td>
   <td style="text-align:left;"> 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;"> 18/11/2013 </td>
   <td style="text-align:left;"> 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;"> 18/11/2013 </td>
   <td style="text-align:left;"> 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;"> 18/11/2013 </td>
   <td style="text-align:left;"> 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;"> 18/11/2013 </td>
   <td style="text-align:left;"> 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;"> 13/11/2013 </td>
   <td style="text-align:left;"> 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;"> 18/11/2013 </td>
   <td style="text-align:left;"> 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>

- __readr::read_tsv()__ : read tab delimited files
- __readr::read_csv()__ : read comma delimited files

- __readr::write_tsv()__ : write tab delimited files

---

## Excel sheet

---

## Read the data - read_excel

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

<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>

## Writing to Excel file

* - __openxlsx::write.xlsx()__ : write Excel file

---
layout: true

# ggplot2

---

@allison_horst

---
## 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-02-data_visualization_files/figure-html/unnamed-chunk-30-1.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

---

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

.right-plot[
<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-32-1.png" width="70%" style="display: block; margin: auto;" />
]

---

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

.right-plot[
<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-33-1.png" width="70%" style="display: block; margin: auto;" />
]

---

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

.right-plot[
<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-34-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Make dot size bigger

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

.right-plot[
<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-35-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Make dot size bigger

```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-02-data_visualization_files/figure-html/unnamed-chunk-36-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Color according to depth level (discrete)

```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-02-data_visualization_files/figure-html/unnamed-chunk-37-1.png" width="70%" style="display: block; margin: auto;" />
]

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

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

.right-plot[
<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-38-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Symbol according to transect (continuous)

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

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

<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-39-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Symbol according to transect (continuous)

```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-02-data_visualization_files/figure-html/unnamed-chunk-40-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Panels depending on one variable

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

.right-plot[
<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-41-1.png" width="70%" style="display: block; margin: auto;" />
]

---
## Adding a regression line

```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-02-data_visualization_files/figure-html/unnamed-chunk-42-1.png" width="70%" style="display: block; margin: auto;" />
]

---
## Adding a regression line

```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-02-data_visualization_files/figure-html/unnamed-chunk-43-1.png" width="70%" style="display: block; margin: auto;" />
]

---

## Finalizing the graph

```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-02-data_visualization_files/figure-html/unnamed-chunk-44-1.png" width="70%" style="display: block; margin: auto;" />
]

---
exclude: true

# Putting several graphs together

---
exclude: true

## First graph

```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-02-data_visualization_files/figure-html/unnamed-chunk-45-1.png" width="70%" style="display: block; margin: auto;" />
]

---
exclude: true

## Second graph

```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
```

]

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<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-46-1.png" width="70%" style="display: block; margin: auto;" />
]

---
exclude: true
## Putting together

```r
cowplot::plot_grid(g1, g2, 
                   nrow = 2, 
                   labels = c("A", "B") ) 
```
* See also package : `gridExtra`
]

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<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-47-1.png" width="70%" style="display: block; margin: auto;" />
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---
layout: true

# ggplot2 syntax

---
## Anatomy of a plot

---

## Geometries

---
## Continuous x and y

---

## Plotting error

---

## Discrete x - Continuous y

---

## Continuous x

---

## 3D

---

## Modifying axis and scales

---

## Palettes

Package tmaptools : https://github.com/mtennekes/tmaptools
* Function : `palette_explorer()`

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

---

## Themes

---

## Extensions

http://www.ggplot2-exts.org/gallery/

---
layout: false

# What did you learn ?

---
<br>
<br>
<br>

.font150[
- Grammar of graphics
]
--
.font150[
- Differentiate the elements that are fixed and those that vary (aes)
]

--
.font150[
- Choose the graphics that best suit your purpose
]

---

# Your turn - Write code to reproduce figure below

---

---
exclude: true

```r
ggplot(filter(samples, 
               transect==2 & !is.na(depth)), 
        aes(y=depth, x=picoeuks))  + 
geom_point(size=3)
```

]

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<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-60-1.png" width="70%" style="display: block; margin: auto;" />
]

---
exclude: true

```r
ggplot(filter(samples, 
             transect==2 & !is.na(depth)), 
      aes(y=depth, x=picoeuks))  + 
geom_point(size=3) +
facet_wrap(~ station) 
```

]

.right-plot[
<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-61-1.png" width="70%" style="display: block; margin: auto;" />
]

---
exclude: true

```r
ggplot(filter(samples, 
             transect==2 & !is.na(depth)), 
      aes(y=depth, x=picoeuks))  + 
geom_point(size=3) +
facet_wrap(~ station) +
geom_path() 
```
* Do not use `geom_line`
]

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<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-62-1.png" width="70%" style="display: block; margin: auto;" />
]

---
exclude: true

```r
ggplot(filter(samples, 
             transect==2 & !is.na(depth)), 
      aes(y=depth, x=picoeuks))  + 
geom_point(size=3) +
facet_wrap(~ station) +
geom_path() +
scale_y_reverse()
```

]

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<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-63-1.png" width="70%" style="display: block; margin: auto;" />
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---
exclude: true

]

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<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-64-1.png" width="70%" style="display: block; margin: auto;" />
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---
exclude: true

```r
ggplot(filter(samples, 
             transect==2 & !is.na(depth)), 
      aes(y=depth, x=picoeuks))  + 
geom_point(size=3) +
facet_wrap(~ station) +
geom_path() +
scale_y_reverse() +
theme_bw() +
ggtitle("Percentage of pico-eukaryotes per station on transect 2") +
xlab("Pico-eukaryote per mL") +
ylab("Depth (m)") 
```

]

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<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-65-1.png" width="70%" style="display: block; margin: auto;" />
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---
exclude: true

]

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<img src="R-session-02-data_visualization_files/figure-html/unnamed-chunk-66-1.png" width="70%" style="display: block; margin: auto;" />
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