added tree_subset function #6
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…ching to ensure treeio is installed.
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this function should goes to treeio pkg, as it depends on treeio and the output is also a tree object instead of tbl_tree.
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another reason is that treeio depends on tidytree and tidytree can't depends on treeio, otherwise there will be a circle dependency and all of these pkgs will fail to compile and install.
| dplyr::mutate(isTip = (!node %in% parent)) %>% | ||
| dplyr::filter(isTip) %>% | ||
| dplyr::pull(label) | ||
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do you think group_labels is necessary?
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Do you mean that the entire code chunk seems unnecessary or it is improperly named? I think I agree if the latter, and will rename it to subset_labels but I do think its functionality is necessary as it is the chunk that is isolating the related nodes
| # This drops all of the tips that are not included in group_nodes | ||
| subtree <- treeio:::gfocus(tree, group_labels, "focus") %>% | ||
| treeio:::drop.tip(., .$tip.label[-group_nodes], rooted = TRUE) %>% | ||
| treeio:::groupOTU.phylo(.node = node) |
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the drop.tip function supports treedata object as well as phylo and it would be better to support treedata object to maintain associated data with nodes in the subtree.
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@GuangchuangYu I have started working on the PR for this in the It looks like the Other than that, the PR is almost ready to submit, but I will wait for your feedback before I move forward with it. |
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@tbradley1013 thanks for pointing this out. With the commit, YuLab-SMU/treeio@1c8627e, |
This PR relates to the discussion in #5. It adds a function
tree_subsetthat takes a tree of classphyloand a selected node of said tree and returns a subset of the tree (still with classphylo) with the relatives of the specified node back to a specified level.Tests have also been added to ensure that the expected tips and nodes are added and that the branch lengths are preserved during subsetting.