# INBO CODING CLUB

24 November 2020

Welcome! Welcome! Welcome!

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library(tidyverse)

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## Yellow sticky notes

No yellow sticky notes online. Put your name + " | " and add a "*" each time you solve a challenge (see below).

## Participants

Name | Challenges
--- | ---
Damiano Oldoni |
Dirk Maes | ***
Emma Cartuyvels |***
Lynn Pallemaerts | **
Patrik Oosterlynck | ***
Joost Vanoverbeke | ***
An Leyssen | **
Hans Van Calster | ***
Mathias Wackenier|***
Amber Mertens | ***
Arno Thomaes|*
Anja Leyman |***

## Challenge 1

Damiano's solution:

ggplot(data) + 
    

Joost:

CO2 %>%
  ggplot(aes(conc, uptake, color = Treatment, shape = Type)) +
  geom_point() +
  labs(title = "cold tolerance of the grass species Echinochloa crus-galli",
       y = "CO2 uptake") +
  scale_x_log10() +
  scale_color_manual(values = c("indian red", "blue"))
    

Emma:

ggplot(CO2, aes(x = conc, y = uptake)) +
  geom_point(aes(colour = Treatment, shape = Type)) +
  labs(y = "CO2 uptake",
       title = "cold tolerance of the grass species \n Echinochloa crus-galli") +
  scale_x_log10() +
  scale_color_manual(values = c("indian red", "blue"))

Anja:

ggplot (data = CO2, aes(x = conc,
                        y = uptake,
                        color = Treatment,
                        shape = Type)) +
  geom_point() +
  ylab("CO2 uptake") +
  ggtitle("cold tolerance of the grass species Echinochloa crus-galli") +
  scale_x_log10() +
  scale_color_manual(values=c("indian red", "blue"))
  

Patrik:

ggplot(data = CO2, aes(y =  uptake, x = conc)) + 
  geom_point(aes(color = Treatment, shape = Type)) + 
  ylab("CO2 uptake") + 
  ggtitle("Cold tolerance of the grass species Echinochloa crus-galli") +
  scale_x_log10() +
  scale_color_manual(values=c("indian red", "blue"))

Lynn:

ggplot(data=CO2,
       mapping=aes(x=conc, y=uptake, color=Treatment)) +
  geom_point(aes(shape=factor(Type))) +
  ylab("CO2 uptake") +
  ggtitle("Cold tolerance of the grass species Echinochloa crus-galli") +
  scale_x_log10() +
  scale_color_manual(values=c("blue","indian red"))

Hans:

ggplot(CO2) +
  geom_point(aes(x = conc, y = uptake, color = Treatment, shape = Type)) +
  scale_x_log10(breaks = c(100, 200, 500, 1000)) +
  scale_color_manual(values = c("nonchilled" = "indian red", "chilled" = "blue")) +
  labs(y = "C02 uptake", 
       x = "Concentration", 
       title = expression(
         paste("Cold tolerance of the grass species ",
                italic("Echinochloa crus-galli")))
       )

Amber:

ggplot(data = CO2, 
       mapping = aes(x = conc, y = uptake, color = Treatment, shape = Type)) + 
  geom_point() + 
  scale_x_log10() +
  labs(title = "Cold tolerance of the grass species Echinochloa crus-galli", 
       ylab = "CO2 uptake") + 
  scale_fill_manual(values = c("blue", "indian red"))

### Dirk

Met aanpassen van achtergrond en tekstgrootte op de assen):

p <- ggplot(CO2,
            aes(x = conc,
			    y = uptake,
				colour = Treatment,
				cex = Type)) +
	geom_point() +
	ggtitle("Cold tolerance of the grass species Echinochloa crus-galli") +
	scale_y_log10() +
	scale_color_manual(values = c("chilled" = "blue",
	                            "nonchilled" = "indian red")) +
	xlab("Concentration") +
	ylab("CO2 uptake") +
	theme(axis.text.x = element_text(angle = 45,
                                    hjust = 1),
				axis.text = element_text(size = 20),
				axis.title = element_text(size = 25,
                                        face = "bold"),
				legend.text = element_text(size = 20),
				legend.title = element_text(size = 20), 
				panel.background = element_rect(fill = "white",
                colour = "grey",
                size = 1,
                linetype = "solid"), 
				panel.grid.major = element_line(size = 0.5,
                linetype = "solid",
                colour = "grey"),
				strip.text = element_text(size = 15,
                face = "bold"),
				plot.title = element_text(size = 20,
                face = "bold"))
p

An:

ggplot(data = CO2, 
               mapping = aes(x = conc, y = uptake, 
                             color = Treatment, shape = Type)) + 
  geom_point() +
  ylab("CO2 uptake") +
  ggtitle("cold tolerance of the grass species Echinochloa crus-galli") +
  scale_x_log10() + 
  scale_colour_manual(values = c("chilled" = "blue", "nonchilled" = "indian red"))

## INTERMEZZO

### Example 1

# option 1 (make changes to aesthetics of second geomtry)
ggplot(CO2, aes(x = conc, y = uptake, color = Type)) + 
  geom_violin() + 
  geom_violin(aes(color = NULL), alpha = 0.5)

# option 2 (specify both aesthetics separately)
ggplot(CO2) + 
  geom_violin(aes(x = conc, y = uptake, color = Type)) + 
  geom_violin(aes(x = conc, y = uptake), alpha = 0.5)

# option 3 (specify first the common part of the two aesthetics)
ggplot(CO2, aes(x = conc, y = uptake)) + 
  geom_violin(aes(color = Type)) + 
  geom_violin(alpha = 0.5)

### Example 2

# option 1 (make changes to aesthetics of second geomtry)
ggplot(CO2, aes(x= conc, y = uptake, color = Type, group = Plant)) + 
  geom_line() + 
  geom_smooth(aes(group = NULL, fill = Type))

#option 2 (specify both aesthetics separately)
ggplot(CO2) +
  geom_line(aes(x= conc, y = uptake, color = Type, group = Plant)) + 
  geom_smooth(aes(x= conc, y = uptake, color = Type, fill = Type))

# option 3 (specify first the common part of the two aesthetics)
ggplot(CO2, aes(x= conc, y = uptake, color = Type)) + 
  geom_line(aes(group = Plant)) + 
  geom_smooth(aes(fill = Type))

## Challenge 2

Emma:

ggplot(CO2, aes(x = conc, y = uptake)) +
  geom_point(color = "green", alpha = 0.1)

ggplot(CO2, aes(x = as.factor(conc), y = uptake, fill = Treatment)) +
  geom_boxplot()

Hans:

ggplot(CO2, aes(x = conc, y = uptake)) +
  geom_point(color = "green", alpha = 0.5)


ggplot(CO2, aes(x = conc, y = uptake)) +
  geom_boxplot(aes(group = factor(conc):Treatment,
                   color = Treatment))

Lynn:

ggplot(CO2, aes(x = conc,
                y = uptake)) +
  geom_point(aes(alpha=0.1)) +
  scale_colour_manual(values = c("green"))

ggplot(CO2, aes(x = Treatment,
                y = uptake,
                color=Type )) +
  geom_boxplot()

Amber:

ggplot(CO2, aes(x = conc, y = uptake)) +
  geom_point(color = "green", alpha = 0.1)
  
ggplot(CO2, aes(x = as.factor(conc), y = uptake, color = Treatment)) +
  geom_boxplot()  

Dirk:

p <- ggplot(CO2,
						aes(x = factor(conc),
								y = uptake,
								color = Treatment)) +
  geom_boxplot() +
	ggtitle("Cold tolerance of the grass species Echinochloa crus-galli") +
	scale_y_log10() +
	scale_color_manual(values = c("chilled" = "blue",
																"nonchilled" = "indian red")) +
	xlab("Concentration") +
	ylab("CO2 uptake") +
	theme(axis.text.x = element_text(angle = 45,
																	 hjust = 1),
				axis.text = element_text(size = 20),
				axis.title = element_text(size = 25,
																	face = "bold"),
				legend.text = element_text(size = 20),
				legend.title = element_text(size = 20), 
				panel.background = element_rect(fill = "white",
																				colour = "grey",
																				size = 1,
																				linetype = "solid"), 
				panel.grid.major = element_line(size = 0.5,
																				linetype = "solid",
																				colour = "grey"),
				strip.text = element_text(size = 15,
																	face = "bold"),
				plot.title = element_text(size = 20,
																	face = "bold"))
p

Mathias

#2.1
ggplot(CO2, aes(x = conc, y = uptake)) +
  geom_point(color = "green",
             alpha = 0.1)
#2.2
ggplot(CO2, aes(x = Type, y = uptake))+
  geom_boxplot()+
 ggtitle("CO2 uptake of the grass species Echinochloa crus-galli per type per treatment")
  facet_grid(rows = vars(Treatment))+
  theme(strip.text.y = element_text(angle = 0))

## Challenge 3

Emma:

ggplot(CO2, aes(x = conc, y = uptake, color = Treatment, shape = Type)) +
  geom_point() +
  facet_wrap(~Plant)

area_biotopes <- read_csv("./data/20201124/20201124_area_biotopes.txt", 
                          na = "")

library(INBOtheme)
# New facet label names for region variable
region.labs <- c("Flanders", "South-Netherland", "North-Netherland")
names(region.labs) <- c("FL", "NL_South", "NL_North")

ggplot(area_biotopes,
            aes(x = year,
                y = meanArea,
                colour = species)) +
  geom_pointrange(aes(ymin = meanArea - seArea,
                      ymax = meanArea + seArea)) +
  geom_smooth(se = FALSE) +
  facet_grid(biotope~region,
             labeller = labeller(region = region.labs))

Amber:

ggplot(CO2, aes(x = conc, y = uptake, color = Treatment, shape = Type)) +
  geom_point() +
  facet_wrap(~ Plant)
  
ggplot(area_biotopes,
       aes(x = year,
           y = meanArea,
           colour = species)) +
  geom_pointrange(aes(ymin = meanArea - seArea,
                      ymax = meanArea + seArea)) + 
  geom_smooth() +                    
  facet_grid(biotope ~ region)  

Lynn:

ggplot(CO2, aes(x = conc, y = uptake, color = Treatment, shape = Type)) +
  geom_point() +
  facet_wrap("Plant")
  
  

Hans:

ggplot(CO2, aes(x = conc, y = uptake, color = Treatment, shape = Type)) +
  geom_point() +
  facet_wrap(~ Plant)
  
library(INBOtheme)
ggplot(area_biotopes,
       aes(x = year,
           y = meanArea,
           colour = species)) +
  geom_pointrange(aes(ymin = meanArea - seArea,
                      ymax = meanArea + seArea)) +
  facet_grid(biotope ~ region,
             scales = "free") +
  geom_smooth(se = FALSE)

Anja

 ggplot(CO2, aes(x = conc, y = uptake, color = Treatment, shape = Type)) +
  geom_point() +
  facet_wrap(~Plant)

       aes(x = year,
           y = meanArea,
           colour = species)) +
  geom_pointrange(aes(ymin = meanArea - seArea,
                      ymax = meanArea + seArea)) +
  geom_smooth(se = FALSE) +
  scale_color_manual(values=c("green", "blue")) +
  facet_grid(biotope~region)

Mathias

#3.1
ggplot(CO2, aes(x = conc, y = uptake, color = Treatment, shape = Type)) +
  geom_point()+
  facet_wrap(vars(Plant))
#3.2
ggplot(area_biotopes,
       aes(x = year,
           y = meanArea,
           colour = species)) +
  geom_pointrange(aes(ymin = meanArea - seArea,
                      ymax = meanArea + seArea))+
  geom_smooth(se = FALSE)+
  facet_grid(biotope~region, scales = "free")

## Bonus challenge

Emma:

ggplot(CO2, aes(y = uptake, fill = Treatment:Type)) +
  geom_boxplot(aes(group = Treatment:Type))

ggplot(CO2, aes(x = as.factor(conc), y = uptake)) +
  geom_boxplot() +
  facet_grid(Type~Treatment)

Hans:

ggplot(CO2) +
  geom_boxplot(aes(x = conc,
                   y = uptake,
                   group = factor(conc):Type:Treatment,
                   color = interaction(Type, Treatment, sep = "-"))) +
  labs(x = "concentration", color = "Type-Treatment")

Anja

ggplot(CO2, aes(x = as.factor(conc),
                y = uptake)) +
  geom_boxplot(aes(color = Type:Treatment))
  
  

Amber:

ggplot(CO2, aes(x = as.factor(conc), y = uptake, color = Type:Treatment)) +
  geom_boxplot()