INBO CODING CLUB

# INBO CODING CLUB 17 December 2020 Welcome! ## Share your code snippet If you want to share your code snippet, copy paste your snippet within a section of three backticks (```): As an **example**: ``` library(tidyverse) ``` (*you can copy paste this example and add your code further down*) ## 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 --- | --- Hans Van Calster | Emma Cartuyvels |** Dirk Maes | ** Frieda Van Roy |** An Leyssen |** Arno Thomaes|** Patrik Oosterlynck|** Tom De Dobbelaer |** Karen Cox |** Anja Leyman | ** Leen Govaere |** Stien Heremans | Cécile Herr |** Lynn Pallemaerts | * Luc De Bruyn | ** ## Challenge 1 Hans: ``` code ``` Emma: ``` #' 2. How to use it for user case 1? usercase1 + scale_fill_manual(values = c("#0A831D","#59A648", "#9DC77C","#E9E3BA"), aesthetics = "color") # 2. How to use it for user case 2? usercase2 + scale_fill_gradientn(colors = c("#0A831D","#59A648", "#9DC77C","#E9E3BA"), aesthetics = "fill") ``` Dirk: ``` # usercase 1 library(ggsci) usercase1 <- ggplot(area_biotopes_pararge, aes(x = year, y = meanArea, color = as.factor(biotope))) + geom_point() + geom_smooth() + 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)) + labs(title = "Distribution of Pararge aegeria per biotope and region", y = "Area (%)", x = "Year") + scale_fill_manual("Biotope") + scale_colour_jco() + facet_wrap(~ region) usercase1 ``` ## Challenge 2 Emma: ``` #' `ggplot2` includes some functions to use viridis palette directly. #' 1. How to apply viridis discrete color scale to user case 1? usercase1 + scale_color_viridis_d() #' 2. How to apply viridis continuous color scale to user case 2? usercase2 + scale_fill_viridis_c() #' 3. Invert the color direction. Note: typically inverted color directions are #' less intuitive usercase1 + scale_color_viridis_d(direction = -1) usercase2 + scale_fill_viridis_c(direction = -1) # 4. Use colormap "cividis" instead of default ("viridis") usercase1 + scale_color_viridis_d(option = "E") usercase2 + scale_fill_viridis_c(option = "E") ``` Cécile ``` #' 1. How to apply viridis discrete color scale to user case 1? usercase1_col <- usercase1 + scale_colour_manual(values = viridis(4))) usercase1_col #' 2. How to apply viridis continuous color scale to user case 2? usercase2_col <- usercase2 + scale_fill_gradientn(colors = viridis(4)) usercase2_col #' 3. Invert the color direction. usercase2_col <- usercase2 + scale_fill_gradientn(colors = rev(viridis(4))) usercase2_col # 4. Use colormap "cividis" instead of default ("viridis") usercase2_col <- usercase2 + scale_fill_gradientn(colors = cividis(4)) usercase2_col ``` Anja ``` pal <- viridisLite::viridis(4) pal usercase1 + scale_color_manual(values = pal) sercase2 + scale_fill_gradientn(colours = viridis(4)) #' 3. Invert the color direction. Note: typically inverted color directions are less intuitive usercase1 + scale_color_manual(values = rev(pal)) usercase2 + scale_fill_gradientn(colours = rev(viridis(4))) # 4. Use colormap "cividis" instead of default ("viridis") usercase1 + scale_color_manual(values = cividis(4)) usercase2 + scale_fill_gradientn(colours = cividis(4)) ``` Arno ``` usercase1 + scale_color_viridis(discrete = TRUE) usercase2 + scale_fill_viridis() usercase1 + scale_color_viridis(discrete = TRUE, direction = -1) usercase2 + scale_fill_viridis(direction = -1) usercase1 + scale_color_viridis(discrete = TRUE, option = "cividis") ``` Frieda ``` #' 1. How to apply viridis discrete color scale to user case 1? usercase1 + scale_color_viridis(discrete=TRUE) #' 2. How to apply viridis continuous color scale to user case 2? usercase2 + scale_fill_viridis() #' 3. Invert the color direction. Note: typically inverted color directions are less intuitive usercase1 + scale_color_viridis_d(direction = -1) usercase2 + scale_fill_viridis_c(direction = -1) # 4. Use colormap "cividis" instead of default ("viridis") usercase1 + scale_color_viridis_d(option = "E") usercase2 + scale_fill_viridis_c(option = "E") ``` Lynn ``` #' 1. How to apply viridis discrete color scale to user case 1? usercase1 + scale_color_viridis_d() #' 2. How to apply viridis continuous color scale to user case 2? usercase2 + scale_fill_viridis_c() #' 3. Invert the color direction. Note: typically inverted color directions are less intuitive usercase1 + scale_color_viridis_d(direction=-1) usercase2 + scale_fill_viridis_c(direction=-1) # 4. Use colormap "cividis" instead of default ("viridis") usercase1 + scale_color_viridis_d(option="E") usercase2 + scale_fill_viridis_c(option="E") ``` Tom ``` #' 1. How to apply viridis discrete color scale to user case 1? usercase1+ scale_color_viridis_d() #' 2. How to apply viridis continuous color scale to user case 2? usercase2+ scale_fill_viridis_c() #' 3. Invert the color direction. Note: typically inverted color directions are less intuitive usercase1+ scale_color_viridis_c(direction = -1) usercase2+ scale_fill_viridis_c(direction = -1) # 4. Use colormap "cividis" instead of default ("viridis") usercase2+ scale_fill_gradientn(colours = "cividis") ``` ## INTERMEZZO ## Challenge 3 Cécile: ``` usercase2 <- ggplot(area_biotopes_2010, aes(x = region, y = biotope, group = 1, text = paste("My own text is ", " Mean area: ", meanArea, " Region: ", region, " Biotope: ", biotope))) + geom_tile(aes(fill = meanArea)) + labs(title = "Average covered area (%) in 2010", fill = "Area (%)") + facet_wrap(~ species) ggplotly(usercase2, tooltip = "text") ``` Anja ``` ggplotly(usercase1) ggplotly(usercase2) #' 2. How to personalize the text displayed while hovering on the tiles of usercase2? See example below # region, biotope, value ipv MeanArea, region en Biotope usercase2 <- ggplot(area_biotopes_2010, aes(x = region, y = biotope, text = paste("region: ", region, " biotope: ", biotope, " value: ", round(meanArea, 1) ))) + geom_tile(aes(fill = meanArea)) + labs(title = "Average covered area (%) in 2010", fill = "Area (%)") + facet_wrap(~ species) ggplotly(usercase2, tooltip ="text") usercase1 <- ggplot(area_biotopes_pararge, aes(x = year, y = meanArea, color = as.factor(biotope))) + geom_point(aes(text = paste("year: ", year, " biotope ", biotope, " value: ",round(meanArea, 1) ))) + geom_smooth() + labs(title = "Distribution of Pararge aegeria per biotope and region", y = "Area (%)", color = "BIOTOPE" ) + facet_wrap(~ region) ggplotly(usercase1, tooltip = "text") ``` Emma: ``` #' 1. Make interactive plots for usercase1 and usercase2 using plotly. ggplotly(usercase1) ggplotly(usercase2) #' 2. How to personalize the text displayed while hovering on the tiles of usercase2? #' See example below usercase2 <- ggplot(area_biotopes_2010, aes(x = region, y = biotope, text = paste("region:", region, " biotope:", biotope, " value:", round(meanArea, digits = 1)))) + geom_tile(aes(fill = meanArea)) + labs(title = "Average covered area (%) in 2010", fill = "Area (%)") + facet_wrap(~ species) ggplotly(usercase2, tooltip = "text") # apply the same to usercase1: # hint make sure the "unofficial" aes(text = ...) is only passed on to geom_text usercase1 <- ggplot(area_biotopes_pararge, aes(x = year, y = meanArea, color = as.factor(biotope) )) + geom_point(aes(text = paste("region:", region, " biotope:", biotope, " value:", round(meanArea, digits = 1)))) + geom_smooth() + labs(title = "Distribution of Pararge aegeria per biotope and region", y = "Area (%)", color = "BIOTOPE" ) + facet_wrap(~ region) ggplotly(usercase1, tooltip = "text") ``` Lynn ``` #' 1. Make interactive plots for usercase1 and usercase2 using plotly. ggplotly(usercase1) ggplotly(usercase2) #' 2. How to personalize the text displayed while hovering on the tiles of usercase2? See example below usercase2 <- ggplot(area_biotopes_2010, aes(x = region, y = biotope, group=1, text=paste("region: ", region, " biotope: ", biotope, " value: ", round(meanArea,2)))) + geom_tile(aes(fill = meanArea)) + labs(title = "Average covered area (%) in 2010", fill = "Area (%)") + facet_wrap(~ species) ggplotly(usercase2, tooltip = "text") # apply the same to usercase1: # hint make sure the "unofficial" aes(text = ...) is only passed on to geom_point usercase1 <- ggplot(area_biotopes_pararge, aes(x = year, y = meanArea, color = as.factor(biotope))) + geom_point(aes(text=paste("region: ", region, " biotope: ", biotope, " value: ", round(meanArea,2)))) + geom_smooth() + labs(title = "Distribution of Pararge aegeria per biotope and region", y = "Area (%)", color = "BIOTOPE" ) + facet_wrap(~ region) ggplotly(usercase1, tooltip = "text") ``` Hans ``` #' 1. Make a basic animation plot and set year in the title # step 1 make standard faceted heatmap heatmap_area_biotopes <- ggplot(area_biotopes, aes(x = region, y = biotope)) + geom_tile(aes(fill = meanArea)) + labs(fill = "Area (%)") + facet_wrap(~ species) # step 2 add animation by year heatmap_area_biotopes_animation <- heatmap_area_biotopes + transition_time(time = year) # step 3 set year in the title heatmap_area_biotopes_animation <- heatmap_area_biotopes_animation + ggtitle("Average covered area (%) in {frame_time}", subtitle = "Showing frame {frame} of {nframes}") #' 2. Improve entering and exiting among states heatmap_area_biotopes_animation <- heatmap_area_biotopes_animation + # extra options for improving visualization enter_fade() + exit_shrink() animate(heatmap_area_biotopes_animation, nframes = length(unique(area_biotopes$year)), fps = 1) #' 3. Save animation as gif (default) and set width to 800 pixels and height to 550 pixels anim_save("20201217_animation_heatmap_biotopes.gif", animation = heatmap_area_biotopes_animation, path = "./docs/assets/images/20201217", width = 800, height = 500) #' 4. Do you hate gifs? Well, save the animation as a mp4 video anim_save(filename = "20201217_animation_heatmap_biotopes.mp4", animation = heatmap_area_biotopes_animation, path = "./docs/assets/images/20201217", width = 800, height = 500, renderer = ffmpeg_renderer(format = "mp4")) ``` ## Bonus challenge

Syntax	Example	Reference
# Header	Header	基本排版
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