README.md

In alexwailan/rpinecone: Defines sub-lineages of a clonal expansion via an phylogenetic tree.

rPinecone defines sub-lineages within a bacterial clonal expansion via a phylogenetic tree.

The publication is freely available at https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000264.

Installation

rPinecone is currently available on github. It can be installed with devtools

install.packages("devtools")

devtools::install_github("alexwailan/rpinecone")

Quick Start

Run rPinecone

# devtools::install_github('alexwailan/rpinecone')
library(rPinecone)
library(ape)

tree.file.name <- system.file("extdata", "pyjar.staph_ST2371_45_re_itol_7079_1_6_root.joint.tre", 
    package = "rPinecone")
tree <- ape::read.tree(tree.file.name)
results <- pinecone(tree, 2, 3, quiet = TRUE)

rPinecone, is an R package designed to define sub-lineages within closely related LV populations. rPinecone uses root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node.

Libraries

library(phytools)
library(rPinecone)

The package defines sub-lineages within a bacterial clonal expansion via a phylogenetic tree.

Inputs

• A rooted tree in newick format with branch lengths scaled for SNV distance. A non SNV-scaled tree along with corresponding sequence data can also be provided also to generate the required SNV-scaled tree.

  A SNP scaled tree can be produced using the algorithm of Pupko et al. available in python at pyjar

• SNP threshold - used for sub-grouping

• Relatability threshold - the number of internal vertices/nodes each sub-lineage must have between each other to form a Major Sub-group

Operation

We recommend using the ape package to read in your newick formatted tree.

After loading a tree rPinecone can be called as follows:

tree.file.name <- system.file("extdata", "pyjar.staph_ST2371_45_re_itol_7079_1_6_root.joint.tre", 
    package = "rPinecone")
tree <- ape::read.tree(tree.file.name)
results <- pinecone(tree, 2, 3, quiet = TRUE)

A SNV-scaled tree can also be generated using the function below by taking your tree and corresponding sequence data. The tree is required to be a phylo object and the data requires to be a DNAbin object.

tree <- ace_scale_phylo(tree, data)

Exporting results

iTOL (https://itol.embl.de/) is a web-based tool to visualise phylogenetic trees. This tool also allows users to overlay meta data on the tree through numerous annotation files which can be drag-and-dropped onto the tree. rPinecone is able to output these annotation files in a colour block format for visualisation of Sub-lineags on a phylogenetic tree. rPinecone can also provide a annotation file to replace Tip labels of the tree with the sample's corresponding Sub-group number.

To exports a data file for replacing Tip Labels with Sub-Group number (LABELS) run

itol_labels_template(results)

To export a data file for displaying the Sub-Groups (DATASET_COLOURSTRIP) run

itol_sublineage_output(results)

To export a data file for displaying the Major Sub-Groups (DATASET_COLOURSTRIP) run

itol_major_SL_output(results)

The phylogentic tree with dichotomies resolved into multichotomies can be saved by running

write.tree(results$tree, file = "rpinecone.tree")

Citation

If you use the rPinecone package, please reference the following paper which can be found at the below URL: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000264

Wailan AM, Coll F, Heinz E, Tonkin-Hill G, Corander J, Feasey NA, Thomson NR. 2019. "rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree." Microb Genom. 5(4). doi: [10.1099/mgen.0.000264] (https://doi.org/10.1099/mgen.0.000264)

References

Letunic, Ivica, and Peer Bork. 2007. “Interactive Tree of Life (iTOL): An Online Tool for Phylogenetic Tree Display and Annotation.” Bioinformatics 23 (1): 127–28. doi:10.1093/bioinformatics/btl529.

Paradis, Emmanuel, Julien Claude, and Korbinian Strimmer. 2004. “APE: Analyses of Phylogenetics and Evolution in R Language.” Bioinformatics 20 (2): 289–90. doi:10.1093/bioinformatics/btg412.

Pennell, Matthew W, Jonathan M Eastman, Graham J Slater, Joseph W Brown, Josef C Uyeda, Richard G FitzJohn, Michael E Alfaro, and Luke J Harmon. 2014. “Geiger V2.0: An Expanded Suite of Methods for Fitting Macroevolutionary Models to Phylogenetic Trees.” Bioinformatics 30 (15): 2216–8. doi:10.1093/bioinformatics/btu181.

Revell, Liam J. 2012. “Phytools: An R Package for Phylogenetic Comparative Biology (and Other Things).” Methods Ecol. Evol. 3 (2). Blackwell Publishing Ltd: 217–23. doi:10.1111/j.2041-210X.2011.00169.x.

Schliep, Klaus Peter. 2011. “Phangorn: Phylogenetic Analysis in R.” Bioinformatics 27 (4): 592–93. doi:10.1093/bioinformatics/btq706.

alexwailan/rpinecone documentation built on Sept. 24, 2020, 1:38 p.m.