def qq_plot(hdf5_results_file='/home/bv25/data/Ls154/Ls154_results.hdf5',
png_file_prefix='/home/bv25/data/Ls154/Ls154_results'):
"""
Plot QQ-plot for a single HDF5 result
"""
h5f = h5py.File(hdf5_results_file)
chrom_res_group = h5f['chrom_results']
pvals = [] # sp.empty(h5f['num_snps'][...])
i = 0
for chrom in chrom_res_group.keys():
if chrom != 'chrom_5':
crg = chrom_res_group[chrom]
n = len(crg['ps'])
# pvals[i:i + n] = crg['ps'][...]
pvals.extend(crg['ps'][...].tolist())
i += n
pvals = sp.array(pvals)
quantiles = agr.get_quantiles(pvals)
log_quantiles = agr.get_log_quantiles(pvals, max_val=7)
qq_plot_png_filename = png_file_prefix + '_qq.png'
qq_log_plot_png_filename = png_file_prefix + '_qq_log.png'
agr.simple_qqplot([quantiles], png_file=qq_plot_png_filename)
agr.simple_log_qqplot([log_quantiles],
png_file=qq_log_plot_png_filename,
max_val=7)
def _calculate_qqplot_data_(pvals,num_dots=1000,max_val=6):
quantiles = agr.get_quantiles(pvals, num_dots=num_dots)
exp_quantiles = agr._getExpectedPvalueQuantiles_(num_dots)
log_quantiles = agr.get_log_quantiles(pvals, num_dots=num_dots, max_val=max_val)
exp_log_quantiles = scipy.arange(1, num_dots + 1, dtype='single') / (num_dots + 1) * max_val
quantiles_dict = {'quantiles':quantiles, 'exp_quantiles':exp_quantiles,
'log_quantiles':log_quantiles, 'exp_log_quantiles':exp_log_quantiles}
return quantiles_dict
def _calculate_qqplot_data_(pvals, num_dots=1000, max_val=6):
quantiles = agr.get_quantiles(pvals, num_dots=num_dots)
exp_quantiles = agr._getExpectedPvalueQuantiles_(num_dots)
log_quantiles = agr.get_log_quantiles(pvals,
num_dots=num_dots,
max_val=max_val)
exp_log_quantiles = scipy.arange(1, num_dots + 1,
dtype='single') / (num_dots + 1) * max_val
quantiles_dict = {
'quantiles': quantiles,
'exp_quantiles': exp_quantiles,
'log_quantiles': log_quantiles,
'exp_log_quantiles': exp_log_quantiles
}
return quantiles_dict
def qq_plot(hdf5_results_file='/home/bv25/data/Ls154/Ls154_results.hdf5',
png_file_prefix='/home/bv25/data/Ls154/Ls154_results'):
"""
Plot QQ-plot for a single HDF5 result
"""
h5f = h5py.File(hdf5_results_file)
chrom_res_group = h5f['chrom_results']
pvals = [] # sp.empty(h5f['num_snps'][...])
i = 0
for chrom in chrom_res_group.keys():
if chrom !='chrom_5':
crg = chrom_res_group[chrom]
n = len(crg['ps'])
# pvals[i:i + n] = crg['ps'][...]
pvals.extend(crg['ps'][...].tolist())
i += n
pvals = sp.array(pvals)
quantiles = agr.get_quantiles(pvals)
log_quantiles = agr.get_log_quantiles(pvals, max_val=7)
qq_plot_png_filename = png_file_prefix + '_qq.png'
qq_log_plot_png_filename = png_file_prefix + '_qq_log.png'
agr.simple_qqplot([quantiles], png_file=qq_plot_png_filename)
agr.simple_log_qqplot([log_quantiles], png_file=qq_log_plot_png_filename, max_val=7)