[jiajic]

Stacked on #152 (the showClusterDendrogram() deprecation). The base is that PR's branch. Merge #152 into gsource first and delete its branch, so GitHub retargets this PR to gsource. Otherwise, retarget this PR to gsource by hand before merging it.

Brings plotClusterTree() in line with Giotto's tree consumers after Giotto#1321, where calculateClusterTree() started returning a giottoTree that records what it was built from.

Changes

• Signature: plotClusterTree(gobject, tree, labels = NULL, spat_unit, feat_type, cluster_column = NULL, view = NULL, k, ...).
  • tree is now the second argument.
  • labels is optional. plotClusterTree(g, tree) draws the tree on its own, labelled with the cluster IDs, which makes it the in-suite ggplot replacement for the deprecated showClusterDendrogram().
• Defaults from the tree: cluster_column, spat_unit, feat_type and view default to those recorded on a giottoTree, following the same rule as Giotto:
  • inheriting a view prints a short message
  • an explicit value wins, with a warning when it differs from the tree's
  • a plain hclust needs cluster_column passed explicitly
• view: narrows the cells the size track counts, so counts and tree describe the same cells. Only cell metadata is narrowed, since that's all the plot reads from the object.
• Leaf check: a tree whose leaves don't match the clusters in the data is an error naming "clusters with no leaf" and "leaves with no cells". Before, a leaf with no cells drew as an empty cluster, and a cluster with no leaf was dropped from the counts.
• File rename: R/plot_dendrogram.R → R/plot_cluster_tree.R, with Collate updated. It follows the naming rule: "tree" for the object, "dendrogram" only for the drawing or R's dendrogram class.

The context and leaf-check logic is a short copy of Giotto's (.pct_tree_context(), .pct_check_leaves()). GiottoVisuals can't call Giotto, because Giotto imports GiottoVisuals, so it's duplicated rather than exported from either package.

The unreleased 0.2.16 NEWS bullet for plotClusterTree() is amended in place.

Verification

Four new tests in test-plot-cluster-tree.R:

• a giottoTree renders with neither labels nor cluster_column
• a plain hclust needs cluster_column
• a tree from another clustering is refused at the leaf check
• the view is inherited with a message, and an overriding view warns, then errors at the leaf check because it brings back clusters the tree has no leaf for

All 42 tests pass (91 expectations). The tests call Giotto::calculateClusterTree(view =), which is on Giotto gsource as of #1320.

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