Package: SigTree 1.10.6

SigTree: Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree

Provides tools to identify and visualize branches in a phylogenetic tree that are significantly responsive to some intervention, taking as primary inputs a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip (OTU) labels and p-values.

Authors:John R. Stevens and Todd R. Jones

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SigTree.pdf |SigTree.html✨
SigTree/json (API)
NEWS

# Install 'SigTree' in R:

install.packages('SigTree', repos = c('https://johnrstevens.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

24 exports 0.71 score 88 dependencies 2 mentions 3 scripts 208 downloads

Last updated 7 years agofrom:e1f03b0075. Checks:OK: 1 NOTE: 5 WARNING: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 04 2024
R-4.5-win-x86_64	NOTE	Sep 04 2024
R-4.5-linux-x86_64	NOTE	Sep 04 2024
R-4.4-win-x86_64	NOTE	Sep 04 2024
R-4.4-mac-x86_64	NOTE	Sep 04 2024
R-4.4-mac-aarch64	NOTE	Sep 04 2024
R-4.3-win-x86_64	WARNING	Sep 04 2024
R-4.3-mac-x86_64	WARNING	Sep 04 2024
R-4.3-mac-aarch64	WARNING	Sep 04 2024

Exports:adonis.tree circularplot2 edge.colors export.figtree export.inherit fishers hartung index.matrix node_depth_edgelengthSigTree node_depthSigTree node_height_cladoSigTree node_heightSigTree num.edges num.internal.nodes num.tips num.total.nodes p.p2.ADJ.p1 p2.p1 plotphylo2 plotSigTree result srt.pvalues stouffers tip.colors

Dependencies:ade4 ape askpass Biobase BiocGenerics biomformat Biostrings cli cluster codetools colorspace cpp11 crayon curl data.table digest dplyr fansi farver foreach generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gtable hms httr igraph IRanges isoband iterators jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv mime multtest munsell nlme openssl permute phyext2 phylobase phyloseq pillar pixmap pkgconfig plyr prettyunits progress purrr R6 RColorBrewer Rcpp RcppArmadillo reshape2 rhdf5 rhdf5filters Rhdf5lib rlang rncl RNeXML S4Vectors scales sp stringi stringr survival sys tibble tidyr tidyselect UCSC.utils utf8 uuid vctrs vegan viridisLite withr XML xml2 XVector zlibbioc

SigTree Tutorial Vignette

Rendered fromSigTree.Rnwusingutils::Sweaveon Sep 04 2024.

Last update: 2017-10-02
Started: 2013-12-28

Citation

Readme and manuals

Help Manual

Help page	Topics
Determine significantly responsive branches in phylogenetic trees	SigTree-package SigTree
Function to perform adonis test of independence on p-values from tests of multiple OTUs.	adonis.tree
Function to export a 'NEXUS' file that can be opened in 'FigTree' to produce a plot of the phylogenetic tree with branches colored according to significance of families of p-values	export.figtree
Function to produce a CSV file with the p-value for each branch as well as a list of all of the tips in each branch's family	export.inherit
Function to convert two-tailed p-values to one-tailed, for use by other SigTree functions.	p2.p1
Function to plot the phylogenetic tree in R with branches (tips) colored according to significance of families of p-values (tips' p-values)	plotSigTree
SigTree Other Functions	circularplot2 edge.colors fishers hartung index.matrix node_depthSigTree node_depth_edgelengthSigTree node_heightSigTree node_height_cladoSigTree num.edges num.internal.nodes num.tips num.total.nodes p.p2.ADJ.p1 plotphylo2 result R_init_SigTree srt.pvalues stouffers tip.colors