PDGPlot {MAGNAMWAR} | R Documentation |
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
PDGPlot(pheno_data, mcl_mtrx, 'OG5_126778', 'Treatment', 'RespVar', ylimit=12)