def run(self):
# Module on demand #
from rpy2 import robjects as ro
# Load dataframe #
ro.r("library(vegan)")
ro.r("table = read.table('%s', sep='\t', header=TRUE, row.names='X')" % (self.csv))
# Run computation #
if self.calc_distance: ro.r("nmds = metaMDS(table, distance='horn', trymax=200)")
else: ro.r("nmds = metaMDS(table, trymax=200)")
# Extract result #
ro.r("coord = scores(nmds)")
ro.r("loadings = nmds$species")
# Retrieve values #
self.coords = r_matrix_to_dataframe(ro.r.coord)
# No loadings without distance #
if self.calc_distance: self.loadings = r_matrix_to_dataframe(ro.r.loadings)
else: self.loadings = False
# Plot it #
self.graph.plot()
def run_df(self):
"""Unfortunately this doesn't seem to work (yet)"""
# Module on demand #
from rpy2 import robjects as ro
# Get frame #
self.frame = self.parent.parent.frame
# Call R #
rframe = pandas_df_to_r_df(self.frame)
ro.r("library(vegan)")
nmds = ro.r['metaMDS'](rframe, distance='horn', trymax=200)
# Retrieve values #
self.coords = r_matrix_to_dataframe(ro.r['scores'](nmds))
self.loadings = list(nmds.rx2('species'))
# Plot it #
self.graph.plot()
