Description Usage Arguments Note References Examples
Create a tree figure for visualizing the results of bouth
1 2 3 4 |
bouth.out |
an output object from the |
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. |
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).
Asnicar, F, et al. "Compact graphical representation of phylogenetic data and metadata with GraPhlAn." PeerJ 3 (2015): e1029.
1 2 3 4 5 6 7 8 9 | 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)
|
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