PDGPlot: Plot of a PDG and Data with Standard Error Bars
In MAGNAMWAR: A Pipeline for Meta-Genome Wide Association

Description Usage Arguments Value Examples

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

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

`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)