MAGNAMWAR (version 2.0.4)

PDGPlot: Plot of a PDG and Data with Standard Error Bars

Description

Bar plot of PDG vs phenotype data with presence of taxa in PDG indicated by color

Usage

PDGPlot(data, mcl_matrix, OG = "NONE", species_colname, data_colname,
  xlab = "Taxa", ylab = "Data", ylimit = NULL, tree = NULL,
  order = NULL, main_title = NULL)

Arguments

data

R object of phenotype data

mcl_matrix

AnalyzeOrthoMCL output

OG

optional parameter, a string with the name of chosen group (OG) to be colored

species_colname

name of column in phenotypic data file with taxa designations

data_colname

name of column in phenotypic data file with data observations

xlab

string to label barplot's x axis

ylab

string to label barplot's y axis

ylimit

optional parameter to limit y axis

tree

optional parameter (defaults to NULL) Path to tree file, orders the taxa by phylogenetic distribution, else it defaults to alphabetical

order

vector with order of taxa names for across the x axis (defaults to alpha ordering)

main_title

string for title of the plot (defaults to OG)

Value

a barplot with taxa vs phenotypic data complete with standard error bars

Examples

# NOT RUN {
PDGPlot(pheno_data, mcl_mtrx, 'OG5_126778', 'Treatment', 'RespVar', ylimit=12)

# }