| mgrastPlotPCO {KbaseKit} | R Documentation |
Performs a PCoA analysis on a taxon abundance matrix, using the selected distance metric. Output always produces a .PCoA file that has the normalized eigenvalues (top n lines) and eigenvectors (bottom n x m matrix, n lines) where n is the number of variables (e.g. subsystems), and m the number of samples. You can also choose to produce a .DIST file that contain the distance matrix used to generate the PCoA.
mgrastPlotPCO(file_in, input_dir = "./", output_PCoA_dir = "./", print_dist = FALSE, output_DIST_dir = "./", dist_method = "bray-curtis", headers = FALSE)
file_in |
input filename |
input_dir |
directory path of input file |
output_PCoA_dir |
directory path for .PCoA output file |
print_dist |
whether to print the .DIST output file |
output_DIST_dir |
directory path for .DIST output file |
dist_method |
distance / dissimilarity metric to apply |
headers |
whether to print headers in .PCoA output file |
Returns 0 on success.
Returns -1 when cranky.
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Kevin Keegan, Daniel Braithwaite
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