Introduction | Details on Dendrograms, Scaling, and Plot Layout | Dendrogram Behavior (Rowv, Colv) | Data Scaling (scale) | Color Selection | Plot Layout (Default and Customization) | Note | Load Data | Dendrogram Options | demonstrate the effect of row and column dendrogram options | Reorder dendrogram by branch means rather than sums | Color dendrograms' branches (using dendextend) | plot a sub-cluster using the same color coding as for the full heatmap | Show effect of row and column label rotation | Show effect of offsetRow/offsetCol (only works when srtRow/srtCol is | Show how to use 'extrafun' to replace the 'key' with a scatterplot | show how to customize the color key | Show effect of z-score scaling within columns, blue-red color scale | Correlation Heatmaps | For variable clustering, rather use distance based on cor(): | Interactive heatmap.2 using heatmaply | Session Information | References

Introduction | Prerequisites | Acknowledgement | Chaining | A dendrogram is a nested list of lists with attributes | Installation | How to explore a dendrogram's parameters | Taking a first look at a dendrogram | Getting nodes attributes in a depth-first search | How to change a dendrogram | The "set" function | Two simple trees to play with | Setting a dendrogram's labels | Setting a dendrogram's nodes/leaves (points) | Setting a dendrogram's branches | Adjusting all branches | Coloring branches based on clustering | Adjusting branches based on labels | Highlighting branches' different heights using line width and color | Changing a dendrogram's structure | Rotation | Unbranching | Pruning | Collapse branches | Adding extra bars and rectangles | Adding colored rectangles | Adding colored bars | ggplot2 integration | Enhancing other packages | DendSer | gplots | NMF | heatmaply | dynamicTreeCut | pvclust | circlize | Comparing two dendrograms | dendlist | dend_diff | tanglegram | Correlation measures | Global Comparison of two (or more) dendrograms | Distance matrix using dist.dendlist | Correlation matrix using cor.dendlist | Baker's Gamma Index | Cophenetic correlation | The Fowlkes-Mallows Index and the Bk plot | The Fowlkes-Mallows Index | The Bk plot | Session info

Introduction | Installation | Basic usage | Default | Correlation heatmaps | Data transformation (scaling, normalize, and percentize) | scale | normalize | percentize | is.na10 (missing values) | Changing color palettes | Customized dendrograms and annotation | Various seriation options | Customized dendrograms using dendextend | Replicating the dendrogram ordering of heatmap.2 | Adding annotation based on additional factors using RowSideColors | Text annotations | Hover text | ggheatmap | Saving your heatmaply into a file | Sidenotes | Credit | Contact | Latest news | Session info

Introduction | iris - Edgar Anderson's Iris Data | Background | The 3 clusters from the "complete" method vs the real species category | Similarity/difference between various clustering algorithms | Clustering prediction of the 3 species classes | Conclusion | khan - Microarray gene expression data set from Khan et al., 2001. Subset of 306 genes. | Comparing the train vs test dendrograms | votes.repub - Votes for Republican Candidate in Presidential Elections | Heatmap | animals - Attributes of Animals

Introduction | How to colour the labels of a dendrogram by an additional factor variable | How to color a dendrogram's labels according to defined groups? (in R) | How to color a dendrogram's branches/labels based on cluster (i.e.: cutree result) | Change dendrogram's labels | Larger font for leaves in a dendrogram | How to view attributes of a dendrogram | How to color the branches in heatmap.2? | For package developers - how to call imported calls from dendextend 0.18.3? | How to plot a fan (Polar) Dendrogram in R? | A way to calculate lowest value of h in cut that produces groupings of a given minimum size? | Coloring dendrogram's end branches (or leaves) based on column number of data frame in R | Color side bar dendrogram plot | Plot a "mirror" (labels on the left) horizontal dendrogram

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