This is a minimal example of a book based on R Markdown and bookdown (https://github.com/rstudio/bookdown). Please see the page “Get Started” at https://bookdown.org/ for how to compile this example.
+From 66b8a4fa58f738dac8e286d08d263fe10191a335 Mon Sep 17 00:00:00 2001 From: Antoine Neuraz <5528070+aneuraz@users.noreply.github.com> Date: Wed, 30 Oct 2019 14:46:12 +0100 Subject: [PATCH] reorganize --- 01-Introduction.Rmd | 20 + 02-types_data.Rmd | 45 + 01-chapitre1.Rmd => 04-perception.Rmd | 108 +- 05-abstraction.Rmd | 12 + 06-principes_design.Rmd | 12 + 07-donnees_tabulaires.Rmd | 13 + 08-Interaction.Rmd | 12 + 09-donnees_spaciales.Rmd | 12 + 10-Visualiser_network.Rmd | 150 +++ 11-donnees_textuelles.Rmd | 12 + 12-donnees_temporelles.Rmd | 12 + 98-techniques_avancees.Rmd | 1 + README.html | 136 +++ _book/abstraction-de-tache.html | 259 +++++ _book/dataviz.epub | Bin 0 -> 342067 bytes _book/dataviz.pdf | Bin 0 -> 146020 bytes _book/dataviz.tex | 418 +++++++ _book/dataviz_files/figure-html/encode-1.png | Bin 0 -> 303121 bytes .../figure-html/unnamed-chunk-1-1.png | Bin 0 -> 48815 bytes .../figure-html/unnamed-chunk-10-1.png | Bin 0 -> 59028 bytes 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create mode 100644 _bookdown_files/dataviz_files/figure-latex/unnamed-chunk-24-1.pdf create mode 100644 _bookdown_files/dataviz_files/figure-latex/unnamed-chunk-25-1.pdf create mode 100644 _bookdown_files/dataviz_files/figure-latex/unnamed-chunk-26-1.pdf create mode 100644 dataviz.log diff --git a/01-Introduction.Rmd b/01-Introduction.Rmd new file mode 100644 index 0000000..bc5d5ba --- /dev/null +++ b/01-Introduction.Rmd @@ -0,0 +1,20 @@ +--- +title: "Introduction à la visualisation : Quoi? Pourquoi? Qui? Comment?" +author: "Antoine Neuraz" +date: "5/28/2019" +output: + bookdown::html_document2: + code_folding: hide +--- + +# Intro + +```{r , include=FALSE} +knitr::opts_chunk$set(echo = FALSE) +``` + + +## TODO + + + diff --git a/02-types_data.Rmd b/02-types_data.Rmd new file mode 100644 index 0000000..9438305 --- /dev/null +++ b/02-types_data.Rmd @@ -0,0 +1,45 @@ +--- +title: "Types de datasets et types de données" +author: "Antoine Neuraz" +date: "10/30/2019" +output: + bookdown::html_document2: + code_folding: hide +--- + +# Types de datasets et types de données + +## Types de datasets + +### Données tabulaires + +```{r} + +dt <- data.frame(x = rep(1:5, 3), + y = c(rep(1,5), rep(2,5),rep(3,5)), + group = rep(1, 5*3)) +dt$group[8] <- 2 + +ggplot(data = dt, + mapping = aes(x = x, y = y, fill = as.factor(group))) + + geom_tile(color = 'white', size = 2) + + annotate("segment", x=0.2,xend=5,y=3.8,yend=3.8,arrow=arrow(type="closed",length= unit(.4,"cm"))) + + annotate("segment", x=0.2,xend=0.2,y=3.8,yend=1,arrow=arrow(type="closed",length= unit(.4,"cm"))) + + annotate("text", x=3, y=0, label = "Cellule contenant une valeur",hjust=0.5) + + annotate("segment", x=3,xend=3,y=0.2,yend=1.5,arrow=arrow(type="closed", length= unit(.4,"cm"))) + + scale_fill_manual(values = list("lightgrey", "darkred"))+ + scale_x_continuous(position = "top")+ + xlab('Attributs (colonnes)') + + ylab('Items (lignes)') + + theme_modern() + + theme(legend.position = 'none', + axis.text=element_blank(), + axis.line =element_blank()) + +``` + +### TODO + +## Types de données + +### TODO \ No newline at end of file diff --git a/01-chapitre1.Rmd b/04-perception.Rmd similarity index 78% rename from 01-chapitre1.Rmd rename to 04-perception.Rmd index 815603d..b17e4b4 100644 --- a/01-chapitre1.Rmd +++ b/04-perception.Rmd @@ -1,57 +1,41 @@ --- -title: "Chapitre 1" +title: "Perception : système visuel, marques et canaux, couleurs" author: "Antoine Neuraz" -date: "5/28/2019" -output: html_document +date: "10/30/2019" +output: + bookdown::html_document2: + code_folding: hide --- -# Intro - -```{r , include=FALSE} -knitr::opts_chunk$set(echo = FALSE) -``` - ```{r, include=FALSE} library(ggplot2) library(tidyverse) library(see) library(patchwork) -source('R/util_functions.R') +library(vizoR) seed = 44 -my_theme_void <- function(base_size = 11, - base_family = "", - base_line_size = base_size / 170, - base_rect_size = base_size / 170) { - - theme_void(base_size = base_size, - base_family = base_family, - base_line_size = base_line_size) %+replace% - theme( legend.position = "none", - plot.title = element_text(hjust = 0.5) - ) -} - - - ``` +# Perception : système visuel, marques et canaux, couleurs + +## TODO +## Types de marques ```{r} -size <- 100 +size <- list(100, 2) min_x <- 0 max_x <- 1 -outliers <- 2 -p_color <- generate_uniform_dataset( + +p_color <- generate_dataset_uniform( dataset_size = size, min_x = min_x, max_x = max_x, - outliers = outliers, seed = seed ) %>% ggplot( @@ -64,18 +48,17 @@ p_color <- generate_uniform_dataset( ) + geom_point(size = 3) + scale_color_material_d() + - my_theme_void() + + theme_void_complete() + labs(subtitle= "Couleur") #p_color ``` ```{r} -p_angle <- generate_uniform_dataset( +p_angle <- generate_dataset_uniform( dataset_size = size, min_x = min_x, max_x = max_x, - outliers = outliers, seed = seed ) %>% mutate(angle = ifelse(group == "group1", 0, pi / 3)) %>% @@ -91,18 +74,17 @@ p_angle <- generate_uniform_dataset( radius = 0.04, size = .8 ) + - my_theme_void() + + theme_void_complete() + scale_color_material_d() + ggtitle("Angle") #p_angle ``` ```{r} -p_size <- generate_uniform_dataset( +p_size <- generate_dataset_uniform( dataset_size = size, min_x = min_x, max_x = max_x, - outliers = outliers, seed = seed ) %>% mutate(size = ifelse(group == "group1", 2, 3)) %>% @@ -115,7 +97,7 @@ p_size <- generate_uniform_dataset( ) ) + geom_point() + - my_theme_void() + + theme_void_complete() + scale_size(range = c(1, 3)) + ggtitle("Taille") #p_size @@ -123,11 +105,10 @@ p_size <- generate_uniform_dataset( ```{r} -p_grey <- generate_uniform_dataset( +p_grey <- generate_dataset_uniform( dataset_size = size, min_x = min_x, max_x = max_x, - outliers = outliers, seed = seed ) %>% ggplot( @@ -139,18 +120,17 @@ p_grey <- generate_uniform_dataset( ) ) + geom_point(size = 3) + - my_theme_void() + + theme_void_complete() + scale_color_manual(values = c('group2' = 'black', 'group1' = 'lightgrey')) + ggtitle("Luminosité") #p_grey ``` ```{r} -dt <- generate_uniform_dataset( +dt <- generate_dataset_uniform( dataset_size = size, min_x = min_x, max_x = max_x, - outliers = outliers, seed = seed ) %>% mutate(curvature = ifelse(group == "group1", 0, 1)) @@ -169,17 +149,16 @@ p_curve <- dt %>% geom_curve(data = subset(dt, group == 'group1'), curvature = 0) + geom_curve(data = subset(dt, group == 'group2'), curvature = .7) + scale_color_material_d() + - my_theme_void() + + theme_void_complete() + ggtitle("Courbe") #p_curve ``` ```{r} -dt <- generate_uniform_dataset( +dt <- generate_dataset_uniform( dataset_size = size, min_x = min_x, max_x = max_x, - outliers = outliers, seed = seed ) @@ -198,17 +177,16 @@ p_box <- dt %>% geom_segment() + #geom_curve(data = subset(dt, group == 'group2'), curvature = .7) + scale_color_material_d() + - my_theme_void() + + theme_void_complete() + ggtitle("Encapsulage") #p_box ``` ```{r} -p_shape <- generate_uniform_dataset( +p_shape <- generate_dataset_uniform( dataset_size = size, min_x = min_x, max_x = max_x, - outliers = outliers, seed = seed ) %>% ggplot( @@ -221,17 +199,16 @@ p_shape <- generate_uniform_dataset( ) + geom_point(size = 3) + #scale_color_manual(values = c('group2' = 'black', 'group1' = 'lightgrey')) + - my_theme_void() + + theme_void_complete() + ggtitle("Forme") #p_shape ``` ```{r} -p_fill <- generate_uniform_dataset( +p_fill <- generate_dataset_uniform( dataset_size = size, min_x = min_x, max_x = max_x, - outliers = outliers, seed = seed ) %>% ggplot( @@ -244,7 +221,7 @@ p_fill <- generate_uniform_dataset( ) + geom_point(size = 3, shape = 21) + scale_fill_manual(values = c('group2' = 'black', 'group1' = 'white')) + - my_theme_void() + + theme_void_complete() + ggtitle("Remplissage") #p_fill ``` @@ -259,7 +236,6 @@ p_color + p_angle + ``` - ## Mappings in ggplot ```{r} @@ -378,31 +354,3 @@ scale_num + scale_shape + scale_color + plot_layout(ncol = 1) ``` figure from [https://serialmentor.com/dataviz/aesthetic-mapping.html]() - - -```{r} - -dt <- data.frame(x = rep(1:5, 3), - y = c(rep(1,5), rep(2,5),rep(3,5)), - group = rep(1, 5*3)) -dt$group[8] <- 2 - -ggplot(data = dt, - mapping = aes(x = x, y = y, fill = as.factor(group))) + - geom_tile(color = 'white', size = 2) + - annotate("segment", x=0.2,xend=5,y=3.8,yend=3.8,arrow=arrow(type="closed",length= unit(.4,"cm"))) + - annotate("segment", x=0.2,xend=0.2,y=3.8,yend=1,arrow=arrow(type="closed",length= unit(.4,"cm"))) + - annotate("text", x=3, y=0, label = "Cellule contenant une valeur",hjust=0.5) + - annotate("segment", x=3,xend=3,y=0.2,yend=1.5,arrow=arrow(type="closed", length= unit(.4,"cm"))) + - scale_fill_manual(values = list("lightgrey", "darkred"))+ - scale_x_continuous(position = "top")+ - xlab('Attributs (colonnes)') + - ylab('Items (lignes)') + - theme_modern() + - theme(legend.position = 'none', - axis.text=element_blank(), - axis.line =element_blank()) - -``` - - diff --git a/05-abstraction.Rmd b/05-abstraction.Rmd new file mode 100644 index 0000000..ff72422 --- /dev/null +++ b/05-abstraction.Rmd @@ -0,0 +1,12 @@ +--- +title: "Abstraction de tâche" +author: "Antoine Neuraz" +date: "10/30/2019" +output: + bookdown::html_document2: + code_folding: hide +--- + +# Abstraction de tâche + +## TODO diff --git a/06-principes_design.Rmd b/06-principes_design.Rmd new file mode 100644 index 0000000..285db32 --- /dev/null +++ b/06-principes_design.Rmd @@ -0,0 +1,12 @@ +--- +title: "Principes de design" +author: "Antoine Neuraz" +date: "10/30/2019" +output: + bookdown::html_document2: + code_folding: hide +--- + +# Principes de design + +## TODO \ No newline at end of file diff --git a/07-donnees_tabulaires.Rmd b/07-donnees_tabulaires.Rmd new file mode 100644 index 0000000..7a706ce --- /dev/null +++ b/07-donnees_tabulaires.Rmd @@ -0,0 +1,13 @@ +--- +title: "Visualisation de données tabulaires" +author: "Antoine Neuraz" +date: "10/30/2019" +output: + bookdown::html_document2: + code_folding: hide +--- + +# Visualisation de données tabulaires + +## TODO + diff --git a/08-Interaction.Rmd b/08-Interaction.Rmd new file mode 100644 index 0000000..c4fcfa5 --- /dev/null +++ b/08-Interaction.Rmd @@ -0,0 +1,12 @@ +--- +title: "Interaction" +author: "Antoine Neuraz" +date: "10/30/2019" +output: + bookdown::html_document2: + code_folding: hide +--- + +# Interaction + +## TODO \ No newline at end of file diff --git a/09-donnees_spaciales.Rmd b/09-donnees_spaciales.Rmd new file mode 100644 index 0000000..6b14ce2 --- /dev/null +++ b/09-donnees_spaciales.Rmd @@ -0,0 +1,12 @@ +--- +title: "Visualisation de données spatiales" +author: "Antoine Neuraz" +date: "10/30/2019" +output: + bookdown::html_document2: + code_folding: hide +--- + +# Visualisation de données spatiales + +## TODO \ No newline at end of file diff --git a/10-Visualiser_network.Rmd b/10-Visualiser_network.Rmd new file mode 100644 index 0000000..8a42fbe --- /dev/null +++ b/10-Visualiser_network.Rmd @@ -0,0 +1,150 @@ +--- +title: "networks" +author: "Antoine Neuraz" +date: "6/7/2019" +output: html_document +--- + +# Visualisation de réseaux et graphes + +```{r, include = FALSE} + +library(igraph) +library(ggraph) +library(tidygraph) + +nodes <- data.frame(id = c("node1","node2","node3"), + #label = c("node1","node2","node3"), + node_type= rep(1,3)) + +edges <- data.frame(from = c("node1", "node2", "node1" ), + to = c("node2","node3", "node3"), + type = rep("normal",3) , + weight = rep(1,3)) + +``` +```{r} + +``` + + +```{r} + +nodes <- data.frame(id = c("node1","node2","node3"), + #label = c("node1","node2","node3"), + node_type= rep(1,3)) + +edges <- data.frame(from = c("node1", "node2", "node3" ), + to = c("node2","node3", "node1"), + type = rep("normal",3) , + weight = c(3,1,0), + color = c("s","s","h")) + +net <- graph_from_data_frame(d=edges, vertices = nodes, directed = TRUE) + +ggraph(net, layout = "linear", circular = TRUE) + + geom_edge_link(arrow = grid::arrow(type = "closed", length = unit(2,"mm")), + end_cap = circle(5, 'mm'), + start_cap = circle(5, 'mm')) + + geom_node_point(color = 'black', fill ="lightgrey", size = 10, shape = 21) + + expand_limits(y=c(-1.3,1), x = c(-1,1)) + + theme_void() + + theme(legend.position="none") + + theme(plot.margin=unit(c(1,3,1,3),"cm")) +``` + +```{r} + +ggraph(net, layout = "linear", circular = TRUE) + + geom_edge_link(aes(width = weight, color = color)) + + geom_node_point(color = 'black', fill ="lightgrey", size = 10, shape = 21) + + scale_edge_color_manual(values = c('s'="darkgrey", "h" = "white"))+ + expand_limits(y=c(-1.3,1), x = c(-1,1)) + + theme_void() + + theme(legend.position="none") + + theme(plot.margin=unit(c(1,3,1,3),"cm")) + +``` + + + +```{r} +plot(net, + edge.color = 'black', + edge.width = 2, + vertex.label = NA, + vertex.size = 30, + vertex.color = "lightgrey", + vertex.frame.color="black") + +``` + +```{r} + +nodes <- data.frame(id = c("node1","node2","node3", "node4","node5","node6"), + #label = c("node1","node2","node3"), + node_type= c(rep(1,2), rep(2,4)), + node_weight = c(30,20,rep(0,4))) + +edges <- data.frame(from = c("node1", "node1", "node1", "node1", "node1" ), + to = c("node2","node3", "node4", "node5","node6"), + type = c(rep("normal",1), rep('hidden',4)) , + weight = c(3,rep(1,4))) + +net <- graph_from_data_frame(d=edges, vertices = nodes, directed = FALSE) +V(net)$color <- "lightgrey" +V(net)[node_type == 2]$color <- NA +V(net)$frame.color <- "lightgrey" +V(net)[node_type == 2]$frame.color <- NA +V(net)["node1"]$frame.color <- 633 +V(net)["node1"]$size2 <- 8 +V(net)$size <- nodes$node_weight + +E(net)$width <- edges$weight +E(net)$color <- "darkgrey" +E(net)[type == "normal"]$color = 633 + +plot(net, + vertex.label = NA, + ) + +``` + + +```{r} +highschool$size <- abs(rnorm(506)) + +graph <- read_graph("~/Downloads/lesmiserables.gml .webarchive", "gml") + +fills <- V(graph)$fill %>% + as.factor() %>% + levels + +graph_mod <- as_tbl_graph(graph) %>% + activate(nodes) %>% + mutate(size = log(centrality_degree())+0.5) %>% + arrange(desc(group),desc(size)) + +graph_mod %>% + ggraph("linear") + + geom_edge_arc(aes(width = value),color = hsv(0, 0, 0.2, 0.25), fold= TRUE) + + geom_node_point(aes(fill = fill, size =size), shape=21 ) + theme(legend.position="none") + + scale_fill_manual(values = fills) + + geom_node_text(aes(label = label), angle = 90, hjust=1, size = 2.5, nudge_y = -1) + + expand_limits(y=c(-10,NA)) + + theme_void() + theme(legend.position="none") + +``` +```{r} + +graph_mod %>% + ggraph('kk') + + geom_edge_link(aes(width = value),color = hsv(0, 0, 0.2, 0.25), fold= TRUE) + + geom_node_point(aes(fill = fill, size =size), shape=21 ) + theme(legend.position="none") + + scale_fill_manual(values = fills) + + geom_node_text(aes(label = label), repel = TRUE, size = 2) + + expand_limits(y=c(-10,NA)) + + theme_void() + theme(legend.position="none") + +``` + diff --git a/11-donnees_textuelles.Rmd b/11-donnees_textuelles.Rmd new file mode 100644 index 0000000..7a943ae --- /dev/null +++ b/11-donnees_textuelles.Rmd @@ -0,0 +1,12 @@ +--- +title: "Visualisation de texte" +author: "Antoine Neuraz" +date: "10/30/2019" +output: + bookdown::html_document2: + code_folding: hide +--- + +# Visualisation de texte + +## TODO \ No newline at end of file diff --git a/12-donnees_temporelles.Rmd b/12-donnees_temporelles.Rmd new file mode 100644 index 0000000..e904ab7 --- /dev/null +++ b/12-donnees_temporelles.Rmd @@ -0,0 +1,12 @@ +--- +title: "Visualisation de données temporelles" +author: "Antoine Neuraz" +date: "10/30/2019" +output: + bookdown::html_document2: + code_folding: hide +--- + +# Visualisation de texte + +## TODO \ No newline at end of file diff --git a/98-techniques_avancees.Rmd b/98-techniques_avancees.Rmd index 9d3d343..d7d4c2f 100644 --- a/98-techniques_avancees.Rmd +++ b/98-techniques_avancees.Rmd @@ -261,3 +261,4 @@ my_bar(mpg, "drv") + diff --git a/README.html b/README.html new file mode 100644 index 0000000..4c14d41 --- /dev/null +++ b/README.html @@ -0,0 +1,136 @@ + + +
+ + + +This is a minimal example of a book based on R Markdown and bookdown (https://github.com/rstudio/bookdown). Please see the page “Get Started” at https://bookdown.org/ for how to compile this example.
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