inspectTaxonomy: Shiny gadget for tree/taxonomy inspection

In jfukuyama/adaptiveGPCA: Adaptive Generalized PCA

Shiny gadget for tree/taxonomy inspection

Description

Shiny gadget that allows users to visualize the scores of the taxa on the agpca axes, their positions on the phylogenetic tree, and their taxonomic assignments.

Usage

inspectTaxonomy(agpcafit, physeq, axes = c(1, 2), br.length = FALSE,
  height = 600)

Arguments

agpcafit	An agpca object, created either by the function adaptivegpca or by visualizeFullFamily.
physeq	A phyloseq object with a tree and a taxonomy table.
axes	The axes to plot, must be a vector of two whole numbers.
br.length	Plot the tree with the branch lengths?
height	The height, in pixels, of the plotting region.

Value

The function will open a browser window showing the tree and the locations of the taxa on the selected agpca axes. "Brushing" over the plot will highlight the positions of the selected taxa on the tree and list their taxonomic assignments. Clicking the "done" button will exit the app and return a data frame containing the positions of the selected taxa on the agpca axes, the taxonomic assignments of the selected taxa, and their names.

Examples

## Not run: 
data(AntibioticPhyloseq)
pp = processPhyloseq(AntibioticPhyloseq)
out.agpca = adaptivegpca(pp$X, pp$Q, k = 2)
treeInspect(out.agpca, AntibioticPhyloseq)

## End(Not run)

jfukuyama/adaptiveGPCA documentation built on Jan. 10, 2023, 3:22 p.m.