def func_callback( query, user ):
from fatools.lib.analytics.dist import get_distance_matrix
from fatools.lib.analytics.nj import plot_nj
haplotype_sets = query.get_filtered_haplotype_sets()
dm = get_distance_matrix(haplotype_sets)
dbh = query.dbh
fso_dir = get_fso_temp_dir(user.login)
tip_label = query.options.get('tip_label', 'S')
label_callback = {
'S': lambda x: dbh.get_sample_by_id(x).code,
'I': None,
'C': lambda x: dbh.get_sample_by_id(x).location.country,
'1': lambda x: dbh.get_sample_by_id(x).location.level1,
'2': lambda x: dbh.get_sample_by_id(x).location.level2,
'3': lambda x: dbh.get_sample_by_id(x).location.level3,
'4': lambda x: dbh.get_sample_by_id(x).location.level4,
}
tree_type = { 'F': 'fan', 'R': 'radial', 'U': 'unrooted'}[query.options.get('tree_type', 'F')]
njplot_png = plot_nj(dm, fso_dir.abspath, 'png',
label_callback = label_callback[tip_label], tree_type=tree_type)
njplot_pdf = plot_nj(dm, fso_dir.abspath, 'pdf',
label_callback = label_callback[tip_label], tree_type=tree_type)
options = { 'png_plot': fso.get_urlpath(njplot_png),
'pdf_plot': fso.get_urlpath(njplot_pdf) }
html, code = format_output( options )
return { 'custom': None,
'options': None,
'title': 'Neighbor-Joining (NJ) Tree Result',
'html': html,
'jscode': code,
'refs': [
'Paradis E., Claude J. & Strimmer K. (2004) '
'APE: analyses of phylogenetics and evolution in R language. '
'<em>Bioinformatics</em>, <strong>20</strong>: 289-290',
'<a href="http://ape-package.ird.fr/">APE website</a>'
],
}
def func_callback( query, user ):
from fatools.lib.analytics.dist import get_distance_matrix, null_distance
from fatools.lib.analytics.ca import mca, plot_pca, format_data
dimension = 2
haplotype_sets = query.get_filtered_haplotype_sets()
dm = get_distance_matrix(haplotype_sets, null_distance)
mca_res = mca(dm)
fso_dir = get_fso_temp_dir(user.login)
plotfile_urls = []
for (ax, ay) in combinations(range( dimension ), 2):
plotfile = fso_dir.abspath + '/' + 'pcoa-%d-%d' % (ax, ay)
plot_png = plot_pca(mca_res, dm, ax, ay, plotfile + '.png')
plot_pdf = plot_pca(mca_res, dm, ax, ay, plotfile + '.pdf')
plotfile_urls.append( (fso.get_urlpath(plot_png), fso.get_urlpath(plot_pdf)) )
mca_data = format_data(mca_res, dm)
data_file = fso_dir.abspath + '/' + 'mca-data.txt'
with open(data_file, 'w') as outfile:
for r in mca_data:
outfile.write( '\t'.join( r ) )
outfile.write( '\n' )
options = { 'plotfile_urls': plotfile_urls, 'data_file': fso.get_urlpath(data_file) }
html, code = format_output( (mca_res, dm), options )
return { 'custom': None,
'options': None,
'title': 'Multiple Correspondence Analysis (MCA) Result',
'html': html,
'jscode': code,
'refs': [
'Lê, S., Josse, J. & Husson, F. (2008). '
'FactoMineR: An R Package for Multivariate Analysis. '
'<em>Journal of Statistical Software</em>. <strong>25(1)</strong>. pp. 1-18.',
'<a href="http://factominer.free.fr/">FactoMineR website</a>'
],
}
def func_callback( query, user ):
from fatools.lib.analytics.dist import get_distance_matrix
from fatools.lib.analytics.ca import pcoa, plot_pca, format_data
dimension = 2
haplotype_sets = query.get_filtered_haplotype_sets()
dm = get_distance_matrix(haplotype_sets)
pca_res = pcoa(dm, dim = dimension)
fso_dir = get_fso_temp_dir(user.login)
plotfile_urls = []
for (ax, ay) in combinations(range( dimension ), 2):
plotfile = fso_dir.abspath + '/' + 'pcoa-%d-%d' % (ax, ay)
plot_png = plot_pca(pca_res, dm, ax, ay, plotfile + '.png')
plot_pdf = plot_pca(pca_res, dm, ax, ay, plotfile + '.pdf')
plotfile_urls.append( (fso.get_urlpath(plot_png), fso.get_urlpath(plot_pdf)) )
pca_data = format_data(pca_res, dm)
data_file = fso_dir.abspath + '/' + 'pcoa-data.txt'
with open(data_file, 'w') as outfile:
for r in pca_data:
outfile.write( '\t'.join( r ) )
outfile.write( '\n' )
options = { 'plotfile_urls': plotfile_urls, 'data_file': fso.get_urlpath(data_file) }
html, code = format_output( (pca_res, dm), options )
return { 'custom': None,
'options': None,
'title': 'Principal Coordinate Analysis (PCoA) Result',
'html': html,
'jscode': code,
}
return ('Principal Coordinate Analysis (PCoA) Result', html, code)