phydataerror: Phylogenetic Tree with Attached Bar Plot and Standard Error...

In corinsexton/MAGNAMWAR: A Pipeline for Meta-Genome Wide Association

Description

Presents data for each taxa including standard error bars next to a phylogenetic tree.

Usage

PhyDataError(phy, data, mcl_matrix, species_colname, data_colname,
  color = NULL, OG = NULL, xlabel = "xlabel", ...)

Arguments

phy	Path to tree file
data	R object of phenotype data
mcl_matrix	AnalyzeOrthoMCL output
species_colname	name of column in data file with taxa designations
data_colname	name of column in data file with data observations
color	optional parameter, (defaults to NULL) assign colors to individual taxa by providing file (format: Taxa | Color)
OG	optional parameter, (defaults to NULL) a string with the names of chosen group to be colored
xlabel	string to label barplot's x axis
...	argument to be passed from other methods such as parameters from barplot() function

Value

A phylogenetic tree with a barplot of the data (with standard error bars) provided matched by taxa.

References

Some sort of reference

Examples

file <- system.file('extdata', 'muscle_tree2.dnd', package='MAGNAMWAR')
PhyDataError(file, pheno_data, mcl_mtrx, species_colname = 'Treatment', data_colname = 'RespVar',
 OG='OG5_126778', xlabel='TAG Content')

corinsexton/MAGNAMWAR documentation built on May 13, 2019, 10:51 p.m.