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Deprecate showClusterDendrogram(); remove create_cluster_dendrogram() - #152
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…ndrogram() Giotto::calculateClusterTree() builds the tree the splits, node markers and annotations use; plot that instead. Drops the dev-only tree = argument.
labels is optional, tree is second, and cluster_column / units / view for the size track default to the tree's. Leaves are checked against the data. Renames plot_dendrogram.R to plot_cluster_tree.R.
…ults plotClusterTree(gobject, tree): defaults from a giottoTree
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showClusterDendrogram()builds and draws a cluster dendrogram.Giotto::calculateClusterTree()now builds that tree better, and other functions depend on its output:getDendrogramSplits(),findNodeMarkers(),writeClusterTreeQuery()andannotateClusterTree()all use.view =(Giotto#1320).showClusterDendrogram()builds its own tree, without the ordering guarantee, so its figure can disagree with the splits, markers and annotations. Given a tree, it amounts toggdendro::ggdendrogram(tree).plot(tree)does the same in base graphics, andplotClusterTree()draws the annotated version.Changes
showClusterDendrogram(): soft-deprecated. It warns with "was deprecated in GiottoVisuals 0.2.16. Please useGiotto::calculateClusterTree()instead. Plot the returned tree withplot()orggdendro::ggdendrogram()." It keeps working until it's removed, because 7 website tutorials call it.tree =removed fromshowClusterDendrogram(). It came in with feat: showClusterDendrogram(tree = ) #146 and has only been on gsource, so the unreleased NEWS bullet that announced it is removed too.create_cluster_dendrogram(): removed. Its only caller wasshowClusterDendrogram(), and its few lines (dcast → cor →hclust→ggdendrogram) are now inline there. GiottoVisuals can't route throughcalculateClusterTree()itself, because Giotto depends on GiottoVisuals, not the reverse.plotClusterTree()'s@seealsono longer points to the deprecated function.Verification
showClusterDendrogram()'sggplot_build()layers are identical to the pre-change build on the visium mini, withh =included.create_cluster_dendrogramis no longer exported, andtreeis gone from the formals.Follow-ups
plotClusterTree(): alabels = NULLdefault, so it can draw an unannotated tree and become the in-suite ggplot replacement. It'll also gainview =for its cell-count track. Both are planned with agiottoTreesubclass in Giotto that records the view a tree was built under.calculateClusterTree()+plot()/plotClusterTree().🤖 Generated with Claude Code