Graphiques sous R et Python dans Rstudio

class: center, middle, inverse, title-slide

# Graphiques sous R et Python dans Rstudio
### Sebastien Foulle
### 25/01/2019

---

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  white-space: pre-wrap;
  box-shadow: 10px 5px 5px lightblue;
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## Contenu du document

On presente dans les slides suivantes les graphiques usuels en R avec *ggplot2* et *patchwork*, et en Python avec *seaborn*, *matplotlib* et *pandas*.

Prerequis pour produire cette presentation **xaringan** avec Rstudio :

- une distribution Python (Anaconda convient tres bien)
- le package R *reticulate* qui permet d'utiliser des objets R dans des chunks Python (syntaxe *r.mon_objet_r*) et inversement (syntaxe *py$mon_objet_python*)

---

## Chargement des packages et donnees

.pull-left[

```r
library("dplyr")

library("ggplot2")
# pour centrer les titres des graphiques ggplot2
theme_update(plot.title = element_text(hjust = 0.5))

# pour la grille de graphiques
library("patchwork")

dtf = reshape2::tips %>% group_by(size, sex) %>% summarise(tip = mean(tip)) %>% ungroup
dir.create("images")

library("reticulate")
# chemin vers l'executable python
use_python("C:/Users/Sebastien/Anaconda3/python.exe")
```

```python
import matplotlib.pyplot as plt
import seaborn as sns
sns.set()
```
]

---

## Les donnees

.pull-left[
<p style="text-align:center"><svg aria-hidden="true" role="img" viewBox="0 0 581 512" style="height:60px;width:68.09px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:blue;overflow:visible;position:relative;"><path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"/></svg></p>

```r
dtf
```

```
# A tibble: 12 x 3
    size sex         tip
   <int> <fct>     <dbl>
 1     1 Female 1.276667
 2     1 Male   1.92    
 3     2 Female 2.528448
 4     2 Male   2.614184
 5     3 Female 3.25    
 6     3 Male   3.476667
 7     4 Female 4.021111
 8     4 Male   4.172143
 9     5 Female 5.14    
10     5 Male   3.75    
11     6 Female 4.6     
12     6 Male   5.85    
```
]

.pull-right[
<p style="text-align:center"><svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:60px;width:52.5px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:gold;overflow:visible;position:relative;"><path d="M439.8 200.5c-7.7-30.9-22.3-54.2-53.4-54.2h-40.1v47.4c0 36.8-31.2 67.8-66.8 67.8H172.7c-29.2 0-53.4 25-53.4 54.3v101.8c0 29 25.2 46 53.4 54.3 33.8 9.9 66.3 11.7 106.8 0 26.9-7.8 53.4-23.5 53.4-54.3v-40.7H226.2v-13.6h160.2c31.1 0 42.6-21.7 53.4-54.2 11.2-33.5 10.7-65.7 0-108.6zM286.2 404c11.1 0 20.1 9.1 20.1 20.3 0 11.3-9 20.4-20.1 20.4-11 0-20.1-9.2-20.1-20.4.1-11.3 9.1-20.3 20.1-20.3zM167.8 248.1h106.8c29.7 0 53.4-24.5 53.4-54.3V91.9c0-29-24.4-50.7-53.4-55.6-35.8-5.9-74.7-5.6-106.8.1-45.2 8-53.4 24.7-53.4 55.6v40.7h106.9v13.6h-147c-31.1 0-58.3 18.7-66.8 54.2-9.8 40.7-10.2 66.1 0 108.6 7.6 31.6 25.7 54.2 56.8 54.2H101v-48.8c0-35.3 30.5-66.4 66.8-66.4zm-6.7-142.6c-11.1 0-20.1-9.1-20.1-20.3.1-11.3 9-20.4 20.1-20.4 11 0 20.1 9.2 20.1 20.4s-9 20.3-20.1 20.3z"/></svg></p>

```python
dtf = r.dtf; dtf.head(4)
```

```
   size     sex       tip
0     1  Female  1.276667
1     1    Male  1.920000
2     2  Female  2.528448
3     2    Male  2.614184
```

```python
dtf_transposees = dtf.pivot(index='size', columns='sex', values='tip'); dtf_transposees.head(4)
```

```
sex     Female      Male
size                    
1     1.276667  1.920000
2     2.528448  2.614184
3     3.250000  3.476667
4     4.021111  4.172143
```
]

---

## Courbes

```r
ggplot(dtf, aes(size, tip, col = sex)) + geom_line()
```

<img src="hebdor_R_Python_graphiques_files/figure-html/unnamed-chunk-6-1.png" width="450px" height="350px" style="display: block; margin: auto;" />
]

```python
sns.lineplot(x="size", y="tip", hue="sex", data=dtf)
plt.show()
```

<img src="images/courbes.jpg" width="400px" height="300px" style="display: block; margin: auto;" />
]

---

## Nuage de points

```r
ggplot(dtf, aes(size, tip, col = sex)) + geom_point()
```

<img src="hebdor_R_Python_graphiques_files/figure-html/unnamed-chunk-10-1.png" width="400px" height="300px" style="display: block; margin: auto;" />
]

```python
sns.scatterplot(x="size", y="tip", hue="sex", data=dtf)
# ou : sns.lmplot("size", "tip", hue="sex", data=dtf)
plt.show()
```

<img src="images/nuage.jpg" width="400px" height="300px" style="display: block; margin: auto;" />
]

---

## Pavage hexagonal

```r
ggplot(dtf, aes(size, tip)) + geom_hex(bins = 6)
```

<img src="hebdor_R_Python_graphiques_files/figure-html/unnamed-chunk-14-1.png" width="400px" height="300px" style="display: block; margin: auto;" />
]

```python
plt.hexbin(dtf['size'], dtf['tip'], gridsize=(5,5), cmap="Blues")
plt.xlabel("size"); plt.ylabel("tip"); plt.title("Avec matplotlib"); plt.colorbar(); plt.show()
```

<img src="images/pavage.jpg" width="400px" height="300px" style="display: block; margin: auto;" />
]

---

## Diagramme en barres groupees

```r
ggplot(dtf, aes(size, tip, fill = sex)) + geom_col(position = "dodge")
```

<img src="hebdor_R_Python_graphiques_files/figure-html/unnamed-chunk-18-1.png" width="400px" height="300px" style="display: block; margin: auto;" />
]

```python
sns.barplot(x="size", y="tip", hue="sex", data=dtf)
plt.show()
```

<img src="images/barplot_groupe.jpg" width="400px" height="300px" style="display: block; margin: auto;" />
]

---

## Diagramme en barres empilees

```r
ggplot(dtf, aes(size, tip, fill = sex)) + geom_col()
```

<img src="hebdor_R_Python_graphiques_files/figure-html/unnamed-chunk-22-1.png" width="400px" height="300px" style="display: block; margin: auto;" />
]

```python
dtf_transposees.plot.bar(stacked="True", rot = 0)
plt.title("Avec pandas"); plt.show()
```

<img src="images/barplot_empilees.jpg" width="400px" height="300px" style="display: block; margin: auto;" />
]

---

## Histogramme

```r
ggplot(dtf, aes(tip)) + geom_histogram(bins = 4)
```

<img src="hebdor_R_Python_graphiques_files/figure-html/unnamed-chunk-26-1.png" width="400px" height="300px" style="display: block; margin: auto;" />
]

```python
dtf.tip.hist(bins = 4) # ou : sns.distplot(dtf.tip)
plt.title("Avec pandas"); plt.show()
```

<img src="images/histo.jpg" width="400px" height="300px" style="display: block; margin: auto;" />
]

---

## Courbes de densite

```r
ggplot(dtf, aes(tip, fill= sex)) + geom_density(alpha= 0.4)
```

<img src="hebdor_R_Python_graphiques_files/figure-html/unnamed-chunk-30-1.png" width="400px" height="300px" style="display: block; margin: auto;" />
]

```python
sns.kdeplot(data= dtf, x= 'tip', hue= 'sex', shade= True)
plt.show()
```

<img src="images/densite.jpg" width="400px" height="300px" style="display: block; margin: auto;" />
]

---

## Boxplots

```r
ggplot(dtf, aes(sex, tip, fill = sex)) + geom_boxplot()
```

<img src="hebdor_R_Python_graphiques_files/figure-html/unnamed-chunk-34-1.png" width="400px" height="300px" style="display: block; margin: auto;" />
]

```python
sns.boxplot(x="sex", y="tip", data=dtf)
plt.show()
```

<img src="images/boxplots.jpg" width="400px" height="300px" style="display: block; margin: auto;" />
]

---

## Faceting

```r
ggplot(dtf, aes(size, tip))+geom_line()+facet_grid(. ~ sex)
```

<img src="hebdor_R_Python_graphiques_files/figure-html/unnamed-chunk-38-1.png" width="400px" height="300px" style="display: block; margin: auto;" />
]

```python
sns.FacetGrid(dtf,col="sex").map(sns.lineplot,"size","tip")
plt.show()
```

<img src="images/facettes.jpg" width="400px" height="300px" style="display: block; margin: auto;" />
]

---

## Grille

```r
ggplot(dtf, aes(size, tip, col = sex)) + geom_point() + ggtitle("nuage") | 
  ggplot(dtf, aes(size, tip, fill = sex)) + geom_col(position = "dodge") + ggtitle("barres")
```

<img src="hebdor_R_Python_graphiques_files/figure-html/unnamed-chunk-42-1.png" width="550px" height="300px" style="display: block; margin: auto;" />
]

```python
f, axes = plt.subplots(1, 2, figsize=(15, 10))
axes[0].set_title('nuage');axes[1].set_title('barres')
sns.barplot(x='size',y='tip',hue='sex',data=dtf,ax=axes[0])
sns.scatterplot(x='size',y='tip',hue='sex',data=dtf,ax=axes[1])
plt.show()
```

<img src="images/grille.jpg" width="400px" height="250px" style="display: block; margin: auto;" />
]