graphlan: Visualizing the results of 'bouth' with GraPhlAn

In yli1992/BOUTH: Bottom-up Tree Hypothesis Tests

Description

Create a tree figure for visualizing the results of bouth

Usage

graphlan(bouth.out, show.leaf = FALSE, output.dir = getwd(),
  graphlan.dir = NULL, clade.separation = NULL, branch.thickness = NULL,
  branch.bracket.depth = NULL, branch.bracket.width = NULL,
  clade.marker.size = NULL)

Arguments

bouth.out	an output object from the bouth function.
show.leaf	a logical value indicating whether or not the leaf nodes are shown in the output figure.
output.dir	the directory for storing the output figure. The default is the current working directory.
graphlan.dir	the directory where the GraPhlAn package is located.

Note

This function is dependent on the python package GraPhlAn. Parameters clade.separation, branch.thickness, branch.bracket.depth, branch.bracket.width, and clade.marker.size can be set the same as in the python package. Details can be found at (https://bitbucket.org/nsegata/graphlan/overview).

References

Asnicar, F, et al. "Compact graphical representation of phylogenetic data and metadata with GraPhlAn." PeerJ 3 (2015): e1029.

Examples

data(IBD)

## performing the one-stage, weighted bottom-up test on the IBD data
test.1 = bouth(anno.table = IBD$tax.table, pvalue.leaves = IBD$pvalue.otus,
na.symbol = "unknown", far = 0.1, is.weighted = TRUE)


## suppose the GraPhlAn package is located at graphlan_directory/
graphlan(bouth.out = test.1, graph.dir = graphlan_directory)

yli1992/BOUTH documentation built on Sept. 14, 2020, 3:18 a.m.