from indspecies import IndSpecies
from matplotlib.backends.backend_pdf import PdfPages
study = '1526'
z = 4
group_names = '_metadata_dryness'
#group_names = '_kmeans5'
ind_cut = 0.7
for c in [0.5, 0.6, 0.7, 0.8, 0.9, 0.97, 0.99]:
pdffile = '/Users/sperez/Desktop/pie_' + study + '_' + group_names + '_' + str(
ind_cut) + '_' + str(c) + '.pdf'
pdf = PdfPages(pdffile)
indspecies = IndSpecies(study, z)
indspecies.find_indspecies(group_names)
indspecies.cut_indicator_otus(ind_cut)
indspecies.get_significant_otus(cutoff=c)
groups = indspecies.compare()
indspecies.get_stats_report()
for group, plot in piechart(z, groups):
if group < 100:
plot.savefig(pdf, format='pdf')
else:
pass
pdf.close()
print '\n\n\n The pdf file with pie charts is ready.'
from indspecies import IndSpecies
from matplotlib.backends.backend_pdf import PdfPages
study = '1526'
z = 4
group_names = '_metadata_dryness'
#group_names = '_kmeans5'
ind_cut = 0.7
for c in [0.5,0.6,0.7,0.8,0.9,0.97,0.99]:
pdffile = '/Users/sperez/Desktop/pie_'+study+'_'+group_names+'_'+str(ind_cut)+'_'+str(c)+'.pdf'
pdf = PdfPages(pdffile)
indspecies = IndSpecies(study, z)
indspecies.find_indspecies(group_names)
indspecies.cut_indicator_otus(ind_cut)
indspecies.get_significant_otus(cutoff = c)
groups = indspecies.compare()
indspecies.get_stats_report()
for group, plot in piechart(z, groups):
if group < 100:
plot.savefig(pdf, format='pdf')
else: pass
pdf.close()
print '\n\n\n The pdf file with pie charts is ready.'
print pdffile
''' Created on 06/05/2014 author: sperez8 Shows how to use IndSpecies class ''' from indspecies import IndSpecies study = '1526' z = 8 indspecies = IndSpecies(study, z) group_names = '_metadata_dryness' table = indspecies.find_indspecies(group_names) indspecies.get_significant_otus(cutoff=0.9) groups = indspecies.compare() print groups
''' Created on 06/05/2014 author: sperez8 Shows how to use IndSpecies class ''' from indspecies import IndSpecies study = '1526' z = 8 indspecies = IndSpecies(study, z) group_names = '_metadata_dryness' table = indspecies.find_indspecies(group_names) indspecies.get_significant_otus(cutoff = 0.9) groups = indspecies.compare() print groups
