class: center, middle, inverse, title-slide # Hierarchical clustering --- # Figure 1a: Example data showing two clusters of observation pairs <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/hierarchical_clustering_1.png" width="100%" /> --- # Figure 1b: Example data showing fusing of one observation into larger cluster <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/hierarchical_clustering_2.png" width="100%" /> --- # plot of chunk heatmap-noclust <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-heatmap-noclust-1.png" width="100%" /> --- # plot of chunk heatmap-clust <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-heatmap-clust-1.png" width="100%" /> --- # plot of chunk plotexample <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-plotexample-1.png" width="100%" /> --- # plot of chunk plotclustex <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-plotclustex-1.png" width="100%" /> --- # plot of chunk cutree <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-cutree-1.png" width="100%" /> --- # plot of chunk h-k-ex-plot <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-h-k-ex-plot-1.png" width="100%" /> --- # plot of chunk h-k-ex-plot <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-h-k-ex-plot-2.png" width="100%" /> --- # plot of chunk plot-clust-method <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-plot-clust-method-1.png" width="100%" /> --- # plot of chunk plot-clust-method <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-plot-clust-method-2.png" width="100%" /> --- # plot of chunk plot-clust-ward <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-plot-clust-ward-1.png" width="100%" /> --- # plot of chunk plot-clust-comp <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-plot-clust-comp-1.png" width="100%" /> --- # plot of chunk plot-clust-single <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-plot-clust-single-1.png" width="100%" /> --- # plot of chunk plot-clust-average <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-plot-clust-average-1.png" width="100%" /> --- # plot of chunk plot-clust-mcq <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-plot-clust-mcq-1.png" width="100%" /> --- # plot of chunk plot-clust-median <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-plot-clust-median-1.png" width="100%" /> --- # plot of chunk plot-clust-centroid <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-plot-clust-centroid-1.png" width="100%" /> --- # plot of chunk plot-clust-dunn <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-plot-clust-dunn-1.png" width="100%" /> --- # plot of chunk dunn-ex <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/rmd-09-dunn-ex-1.png" width="100%" /> --- # Figure 3: Dunn index increases with increasing number of clusters <img src="data:image/png;base64,#/home/alan/Documents/github/carpentries/high-dimensional-stats-r/fig/hierarchical_clustering_3.png" width="100%" /> ---