{"id":10240,"date":"2019-10-25T19:25:08","date_gmt":"2019-10-25T17:25:08","guid":{"rendered":"https:\/\/www.datanovia.com\/en\/?p=10240"},"modified":"2019-10-26T19:51:35","modified_gmt":"2019-10-26T17:51:35","slug":"clustering-utilisant-la-correlation-comme-mesure-de-distance-dans-r","status":"publish","type":"post","link":"https:\/\/www.datanovia.com\/en\/fr\/blog\/clustering-utilisant-la-correlation-comme-mesure-de-distance-dans-r\/","title":{"rendered":"Clustering utilisant la Corr\u00e9lation comme mesure de Distance dans R"},"content":{"rendered":"<div id=\"rdoc\">\n<p>Diff\u00e9rentes <a href=\"\/?p=7645\">mesures de distance<\/a>\u00a0sont disponibles pour l\u2019analyse de clustering. Cet article d\u00e9crit comment effectuer un <strong>clustering dans R en utilisant la corr\u00e9lation<\/strong> comme mesure de distance.<\/p>\n<p>Contents:<\/p>\n<div id=\"TOC\">\n<ul>\n<li><a href=\"#prerequis\">Pr\u00e9requis<\/a><\/li>\n<li><a href=\"#donnees-de-demonstration\">Donn\u00e9es de d\u00e9monstration<\/a><\/li>\n<li><a href=\"#dessiner-des-heatmaps-a-laide-de-pheatmap\">Dessiner des heatmaps \u00e0 l\u2019aide de pheatmap<\/a><\/li>\n<li><a href=\"#dessiner-des-heatmaps-a-laide-de-gplots\">Dessiner des heatmaps \u00e0 l\u2019aide de gplots<\/a><\/li>\n<li><a href=\"#resume\">R\u00e9sum\u00e9<\/a><\/li>\n<li><a href=\"#voir-aussi\">Voir aussi<\/a><\/li>\n<\/ul>\n<\/div>\n<div id=\"prerequis\" class=\"section level2\">\n<h2>Pr\u00e9requis<\/h2>\n<p>Les packages R suivants seront utilis\u00e9s:<\/p>\n<ul>\n<li><code>pheatmap<\/code> [package pheatmap] : Cr\u00e9e de jolies heatmaps.<\/li>\n<li><code>heatmap.2()<\/code> [package gplots] : Une autre alternative pour cr\u00e9er des heatmaps.<\/li>\n<\/ul>\n<\/div>\n<div id=\"donnees-de-demonstration\" class=\"section level2\">\n<h2>Donn\u00e9es de d\u00e9monstration<\/h2>\n<p>G\u00e9n\u00e9rer un jeu de donn\u00e9es de d\u00e9monstration:<\/p>\n<pre class=\"r\"><code>set.seed(123)\r\nmydata &lt;- matrix(rnorm(200), 20, 10)\r\nmydata[1:10, seq(1, 10, 2)] = mydata[1:10, seq(1, 10, 2)] + 3\r\nmydata[11:20, seq(2, 10, 2)] = mydata[11:20, seq(2, 10, 2)] + 2\r\nmydata[15:20, seq(2, 10, 2)] = mydata[15:20, seq(2, 10, 2)] + 4\r\ncolnames(mydata) = paste(\"Sple\", 1:10, sep = \"\")\r\nrownames(mydata) = paste(\"Gene\", 1:20, sep = \"\")\r\nhead(mydata[, 1:4], 4)<\/code><\/pre>\n<pre><code>##       Sple1  Sple2 Sple3  Sple4\r\n## Gene1  2.44 -1.068  2.31  0.380\r\n## Gene2  2.77 -0.218  2.79 -0.502\r\n## Gene3  4.56 -1.026  1.73 -0.333\r\n## Gene4  3.07 -0.729  5.17 -1.019<\/code><\/pre>\n<p>Pr\u00e9parez vos donn\u00e9es comme d\u00e9crit \u00e0: <a href=\"\/?p=7644\">Pr\u00e9paration des donn\u00e9es et packages R pour l\u2019analyse des clusters<\/a><\/p>\n<\/div>\n<div id=\"dessiner-des-heatmaps-a-laide-de-pheatmap\" class=\"section level2\">\n<h2>Dessiner des heatmaps \u00e0 l\u2019aide de pheatmap<\/h2>\n<p>Par d\u00e9faut, la distance euclidienne est utilis\u00e9e comme mesure de dissimilarit\u00e9.<\/p>\n<pre class=\"r\"><code>library(\"pheatmap\")\r\npheatmap(mydata, scale = \"row\")<\/code><\/pre>\n<p><img decoding=\"async\" src=\"https:\/\/www.datanovia.com\/en\/wp-content\/uploads\/dn-tutorials\/r-tutorial\/figures\/clustering-using-correlation-as-distance-measure-in-r-pheatmaps-1.png\" width=\"480\" \/><\/p>\n<p>Utiliser la corr\u00e9lation comme mesure de dissimilarit\u00e9:<\/p>\n<pre class=\"r\"><code># Corr\u00e9lation par paires entre les \u00e9chantillons (colonnes)\r\ncols.cor &lt;- cor(mydata, use = \"pairwise.complete.obs\", method = \"pearson\")\r\n# Corr\u00e9lation par paires entre les lignes (g\u00e8nes)\r\nrows.cor &lt;- cor(t(mydata), use = \"pairwise.complete.obs\", method = \"pearson\")\r\n\r\n# Cr\u00e9er le heatmap\r\nlibrary(\"pheatmap\")\r\npheatmap(\r\n  mydata, scale = \"row\", \r\n  clustering_distance_cols = as.dist(1 - cols.cor),\r\n  clustering_distance_rows = as.dist(1 - rows.cor)\r\n  )<\/code><\/pre>\n<p><img decoding=\"async\" src=\"https:\/\/www.datanovia.com\/en\/wp-content\/uploads\/dn-tutorials\/r-tutorial\/figures\/clustering-using-correlation-as-distance-measure-in-r-pheatmaps-clustering-correlation-1.png\" width=\"480\" \/><\/p>\n<\/div>\n<div id=\"dessiner-des-heatmaps-a-laide-de-gplots\" class=\"section level2\">\n<h2>Dessiner des heatmaps \u00e0 l\u2019aide de gplots<\/h2>\n<p>Heatmap par d\u00e9faut utilisant la distance euclidienne comme mesure de dissimilarit\u00e9.<\/p>\n<pre class=\"r\"><code>library(\"gplots\")\r\nheatmap.2(mydata, scale = \"row\", col = bluered(100), \r\n          trace = \"none\", density.info = \"none\")<\/code><\/pre>\n<p><img decoding=\"async\" src=\"https:\/\/www.datanovia.com\/en\/wp-content\/uploads\/dn-tutorials\/r-tutorial\/figures\/clustering-using-correlation-as-distance-measure-in-r-gplots-heatmap-2-1.png\" width=\"480\" \/><\/p>\n<p>Utiliser la corr\u00e9lation comme mesure de dissimilarit\u00e9:<\/p>\n<pre class=\"r\"><code># Corr\u00e9lation par paires entre les \u00e9chantillons (colonnes)\r\ncols.cor &lt;- cor(mydata, use = \"pairwise.complete.obs\", method = \"pearson\")\r\n# Corr\u00e9lation par paires entre les lignes (g\u00e8nes)\r\nrows.cor &lt;- cor(t(mydata), use = \"pairwise.complete.obs\", method = \"pearson\")\r\n\r\n## Clustering par ligne et par colonne \u00e0 l'aide d'une corr\u00e9lation \r\nhclust.col &lt;- hclust(as.dist(1-cols.cor)) \r\nhclust.row &lt;- hclust(as.dist(1-rows.cor))\r\n\r\n\r\n# Cr\u00e9er le heatmap\r\nlibrary(\"gplots\")\r\nheatmap.2(mydata, scale = \"row\", col = bluered(100), \r\n          trace = \"none\", density.info = \"none\",\r\n          Colv = as.dendrogram(hclust.col),\r\n          Rowv = as.dendrogram(hclust.row)\r\n          )<\/code><\/pre>\n<p><img decoding=\"async\" src=\"https:\/\/www.datanovia.com\/en\/wp-content\/uploads\/dn-tutorials\/r-tutorial\/figures\/clustering-using-correlation-as-distance-measure-in-r-gplots-heatmap-2-clustering-correlation-1.png\" width=\"480\" \/><\/p>\n<\/div>\n<div id=\"resume\" class=\"section level2\">\n<h2>R\u00e9sum\u00e9<\/h2>\n<p>Dans cet article, nous pr\u00e9sentons comment effectuer une analyse de clustering et dessiner des heatmaps dans R en utilisant les packages <code>pheatmap<\/code> et <code>gplots<\/code><\/p>\n<\/div>\n<div id=\"voir-aussi\" class=\"section level2\">\n<h2>Voir aussi<\/h2>\n<ul>\n<li><a href=\"\/?p=7693\">Heatmap dan R : Visualisation statique et interactive<\/a><\/li>\n<li><a href=\"https:\/\/www.datanovia.com\/en\/blog\/cluster-analysis-in-r-practical-guide\/\">Guide pratique du clustering dans R<\/a><\/li>\n<\/ul>\n<\/div>\n<\/div>\n<p><!--end rdoc--><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Diff\u00e9rentes mesures de distance\u00a0sont disponibles pour l\u2019analyse de clustering. Cet article d\u00e9crit comment effectuer un clustering dans R en utilisant la corr\u00e9lation comme mesure de distance. Contents: Pr\u00e9requis Donn\u00e9es de [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":10241,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"rating_form_position":"","rating_results_position":"","mr_structured_data_type":"","footnotes":""},"categories":[274],"tags":[],"class_list":["post-10240","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-clustering"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v25.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Clustering utilisant la Corr\u00e9lation comme mesure de Distance dans R - Datanovia<\/title>\n<meta name=\"description\" content=\"Dans cet article, nous pr\u00e9sentons comment effectuer une analyse de clustering et dessiner des heatmaps dans R en utilisant les packages pheatmap et gplots\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, 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