def make_pcoa_webgl_string_from_files(pcoa_headers, points, pct_var, map_headers, map_data):
"""make a WebGL representation of a pcoa plot with the provided data
Input:
pcoa_headers: list of headers of a pcoa file
points: coordinates of a pcoa file
map_headers: list of headers for a mapping file
map_data: list of lists containing the data of a mapping file
Output:
webgl_string: string representation of the pcoa plot for WebGL display
"""
ellipses = {}
for h,p in zip(pcoa_headers, points):
ellipses[h] = { 'axes_radii': [0.0, 0.0, 0.0], 'center': p[:3] }
# check the ellipses are created correctly
if ellipses == {}:
raise ValueError, 'Could not create PCoA plot'
webgl_string = make_pcoa_plot(ellipses, (map_data, map_headers), pct_var[:3])
return webgl_string
def generate_pcoa_cloud_from_point_in_omega(mapping_file_tuple, biom_object,
metric, sequences, iterations, axes,
tree_object=None):
"""run the randomisations and get a WebGL PCoA plot string representation
Input:
mapping_file_tuple: data and headers tuple for representing the mapping file
biom_object: otu table biom object
metric: string of the name for the beta diversity metric, i. e. 'unifrac'
sequences: number of sequences per sample
iterations: number of iterations to generate the pcoa plot
axes: number of axes to account for
tree_object: tree to perform the beta diversity calculation
Output:
WebGL string representing the PCoA plot
"""
# get a list of the SampleIds
full_id_list = mapping_file_to_dict(mapping_file_tuple[0], mapping_file_tuple[1]).keys()
pcoa_list = []
for i in range(iterations):
rare_biom_table = get_rare_data(biom_object, sequences)
beta_dm = single_object_beta(rare_biom_table, metric, tree_object)
pcoa_results = pcoa(beta_dm)
pcoa_list.append(pcoa_results)
# convert the list of pcoa lines into ellipsoid coords
ellipse_coords_by_sampleId, sampleId_to_coords = get_pcoa_ellipsoid_coords(pcoa_list, axes, full_id_list)
# check the ellipses are created correctly
if type(ellipse_coords_by_sampleId) == type(''):
raise ValueError, 'Could not create PCoA plot'
webgl_string = make_pcoa_plot(ellipse_coords_by_sampleId, mapping_file_tuple, sampleId_to_coords['variation explained'])
return webgl_string
