MAGNAMWAR (version 2.0.4)

PhyDataError: Phylogenetic Tree with Attached Bar Plot and Standard Error Bars

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

# NOT RUN {
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')

# }