batchAstral: batchAstral

In chutter/AstralPlane: R Package For Preparing, Running, Analyzing and Plotting for the Species Tree Program ASTRAL-III

batchAstral

Description

Function for running many astral analyses across many datasets. Runs setupAstral and runAstral when given a folder that contains folders of gene trees.

Usage

batchAstral(
  genetree.datasets = NULL,
  output.dir = NULL,
  overwrite = FALSE,
  taxa.remove = NULL,
  min.n.samples = 4,
  min.sample.prop = NULL,
  make.polytomy = TRUE,
  polytomy.limit = 0,
  astral.path = NULL,
  astral.t = 2,
  quiet = TRUE,
  multi.thread = TRUE,
  memory = "1g"
)

Arguments

genetree.datasets	a folder with folders of genetrees to prepare for astral analyses
output.dir	the save name for the output directory
overwrite	whether to overwrite an existing dataset
taxa.remove	species that you would like removed from each gene tree
min.n.samples	the minimum number of samples to keep a gene tree
min.sample.prop	the minimum proportion of samples to keep a gene tree
make.polytomy	whether to collapse poorly supported nodes into polytomies
polytomy.limit	if make.polytomy = TRUE, the threshold value for node collapsing
astral.path	the absolute path to astral. Needed because astral needs it.
astral.t	the t value from astral for different annotations.
quiet	hides the screen output from astral if desired
multi.thread	whether to use Astral-MP multithreading or not.
memory	memory value to be passed to java. Should be in "Xg" format, X = an integer

Value

applies setupAstral and runAstral to a folder, that contains folders of gene trees. Facilitates running the preparation and ASTRAL-III analysis for many different datasets at once. Genetree files and the astral output are saved in the desired output directory that can be read in individually as an AstralPlane object and plooted using AstralProjection.

Examples

genetree.folder = "file/path/to/folder/of/genetree/folders"
taxa.delete = c("species_one", "species_two")

batchAstral(genetree.datasets = genetree.folder,
            output.dir = "test-dataset",
            overwrite = TRUE,
            taxa.remove = taxa.delete,
            min.n.samples = 4,
            min.sample.prop = 0.1,
            make.polytomy = TRUE,
            polytomy.limit = 10,
            astral.path = astral.path,
            astral.t = 2,
            quiet = F,
            multi.thread = TRUE,
            memory = "8g")

chutter/AstralPlane documentation built on Aug. 29, 2024, 5:21 p.m.