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Add composition fan tree, ANCOM-BC2 volcano, and MicrobiotaProcess difftree - #10
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…difftree. The default differential tree is now an abundance heatmap. df2volcano fits ANCOMBC::ancombc2, and engine = "microbiota" draws the biomarker tree when MicrobiotaProcess is installed. Co-authored-by: dvsmutin <dvsmutin@gmail.com>
Current ancombc2 pulls microbiome only for phyloseq input. Older releases still receive a phyloseq object. Co-authored-by: dvsmutin <dvsmutin@gmail.com>
A one-column metadata table drops to a vector when ANCOMBC subsets samples, so the group column was missing. Co-authored-by: dvsmutin <dvsmutin@gmail.com>
dsmutin
marked this pull request as ready for review
September 25, 2026 15:31
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Summary
df2composition_tree()draws a ggtree fan cladogram (open.angle = 10,rotate_tree(-90)) with a ggtreeExtra boxplot of relative abundance, coloured by phylum when a rank table is available. References: Yu et al. 2017 (ggtree) and Xu et al. 2021 (ggtreeExtra).df2volcano()fitsANCOMBC::ancombc2on raw counts. The firstlegend_detectpattern is the reference. Current ANCOMBC receives a count matrix and sample metadata, so the check does not need themicrobiomepackage. Older ANCOMBC receives a phyloseq object. Taxa absent from one group are omitted, because ANCOM-BC2 stops when their sampling variance is zero.df2difftree()defaults to a relative-abundance heatmap;fruit = "bar"keeps the fold-change column.engine = "microbiota"runsMicrobiotaProcess::mp_diff_analysisand draws the vignette biomarker tree (radial ggtree, phylum highlight, abundance stars, LDA, FDR). MicrobiotaProcess, ggstar, and phyloseq are optional Suggests.Test plan
fruit = "bar"buildengine = "microbiota"builds a ggtree on the Kraken genus counts