def create_score_distribution_html(fits, use_correlations, dirname):
ensure_dir(dirname)
with interactive(False):
hist_filename = 'R2-hist.png'
fig = plot_score_distribution(fits,use_correlations)
save_figure(fig, join(dirname,hist_filename), b_close=True)
if use_correlations:
scatter_filename = 'comparison-scatter.png'
fig = plot_score_comparison_scatter_for_correlations(fits)
save_figure(fig, join(dirname,scatter_filename), b_close=True)
delta_hist_filename = 'R2-delta-hist.png'
fig = plot_score_improvement_histogram_for_correlations(fits)
save_figure(fig, join(dirname,delta_hist_filename), b_close=True)
image_size = "50%"
from jinja2 import Template
import shutil
html = Template("""
<html>
<head>
<link rel="stylesheet" type="text/css" href="score-distribution.css">
</head>
<body>
<center><H1>R2 Score Distribution</H1></center>
<a href="{{hist_filename}}"> <img src="{{hist_filename}}" height="{{image_size}}"></a>
{% if use_correlations %}
<a href="{{delta_hist_filename}}"> <img src="{{delta_hist_filename}}" height="{{image_size}}"></a>
<a href="{{scatter_filename}}"> <img src="{{scatter_filename}}" height="{{image_size}}"></a>
{% endif %}
</body>
</html>
""").render(**locals())
filename = join(dirname,'scores.html')
with open(filename, 'w') as f:
f.write(html)
shutil.copy(join(resources_dir(),'score-distribution.css'), dirname)
def create_score_distribution_html(fits, use_correlations, dirname):
ensure_dir(dirname)
with interactive(False):
hist_filename = 'R2-hist.png'
fig = plot_score_distribution(fits, use_correlations)
save_figure(fig, join(dirname, hist_filename), b_close=True)
if use_correlations:
scatter_filename = 'comparison-scatter.png'
fig = plot_score_comparison_scatter_for_correlations(fits)
save_figure(fig, join(dirname, scatter_filename), b_close=True)
delta_hist_filename = 'R2-delta-hist.png'
fig = plot_score_improvement_histogram_for_correlations(fits)
save_figure(fig, join(dirname, delta_hist_filename), b_close=True)
image_size = "50%"
import shutil
html = get_jinja_env().get_template('R2.jinja').render(**locals())
filename = join(dirname, 'scores.html')
with open(filename, 'w') as f:
f.write(html)
shutil.copy(join(resources_dir(), 'score-distribution.css'), dirname)
def create_html(data,
fitter,
fits,
basedir,
gene_dir,
exons_dir,
series_dir,
scores_dir,
correlations_dir=None,
use_correlations=False,
link_to_correlation_plots=False,
b_pathways=False,
exons_layout=False,
show_R2=True,
gene_names=None,
region_names=None,
extra_columns=None,
extra_fields_per_fit=None,
extra_top_links=None,
b_inline_images=False,
inline_image_size=None,
b_R2_dist=True,
ttl=None,
top_text=None,
filename=None):
import shutil
if gene_names is None:
gene_names = data.gene_names
if region_names is None:
region_names = data.region_names
if extra_columns is None:
extra_columns = []
if extra_fields_per_fit is None:
extra_fields_per_fit = []
if extra_top_links is None:
extra_top_links = []
if inline_image_size is None:
inline_image_size = '20%'
if ttl is None:
ttl = 'Fits for every Gene and Region'
if filename is None:
filename = 'fits'
if b_pathways:
create_pathway_index_html(data,
fitter,
fits,
basedir,
gene_dir,
series_dir,
use_correlations=use_correlations,
b_unique=True)
create_pathway_index_html(data,
fitter,
fits,
basedir,
gene_dir,
series_dir,
use_correlations=use_correlations,
b_unique=False)
n_ranks = 3 # actually we'll have ranks of 0 to n_ranks
flat_fits = {} # (gene,region) -> fit (may be None)
for g in gene_names:
for r in region_names:
flat_fits[(g, r)] = None
for dsfits in fits.itervalues():
for (g, r), fit in dsfits.iteritems():
if use_correlations:
score = fit.with_correlations.LOO_score
else:
score = fit.LOO_score
fit.score = score
fit.rank = int(np.ceil(n_ranks * score)) if score > 0 else 0
flat_fits[(g, r)] = fit
if exons_layout: #html is organized differently when data is on exons level
scores_per_gene = {}
for (g, r), fit in flat_fits.iteritems():
key = (g[:g.index(cfg.exon_separator)], r)
if fit.score is None:
continue
if key in scores_per_gene:
scores_per_gene[key].append(fit.score)
else:
scores_per_gene[key] = [fit.score]
gene_names = np.lib.arraysetops.unique(
[name[:name.index(cfg.exon_separator)] for name in gene_names])
flat_fits = {}
exons_per_plot = cfg.exons_per_series_plot if 'series' in exons_dir else cfg.exons_per_plot
for (g, r), scores in scores_per_gene.iteritems():
min_score, max_score = min(scores), max(scores)
min_rank = int(np.ceil(n_ranks *
max_score)) if max_score > 0 else 0
max_rank = int(np.ceil(n_ranks *
max_score)) if max_score > 0 else 0
flat_fits[(g, r)] = Bunch(
min_score=min_score,
min_rank=min_rank,
max_score=max_score,
max_rank=max_rank,
num_of_plots=len(scores) / exons_per_plot + 1)
extra_fields_per_fit = list(enumerate(extra_fields_per_fit))
template_file = 'main_exons.jinja' if exons_layout else 'main.jinja'
html = get_jinja_env().get_template(template_file).render(**locals())
filename = join(basedir, '{}.html'.format(filename))
print 'Saving HTML to {}'.format(filename)
with open(filename, 'w') as f:
f.write(html)
shutil.copy(join(resources_dir(), 'fits.css'), basedir)
def create_html(data, fitter, fits,
basedir, gene_dir, series_dir, scores_dir,
correlations_dir = None,
use_correlations = False,
link_to_correlation_plots = False,
b_pathways = False,
show_R2 = True,
gene_names=None, region_names=None,
extra_columns=None, extra_fields_per_fit=None,
extra_top_links=None,
b_inline_images=False, inline_image_size=None,
b_R2_dist=True, ttl=None, top_text=None,
filename=None):
from jinja2 import Template
import shutil
if gene_names is None:
gene_names = data.gene_names
if region_names is None:
region_names = data.region_names
if extra_columns is None:
extra_columns = []
if extra_fields_per_fit is None:
extra_fields_per_fit = []
if extra_top_links is None:
extra_top_links = []
if inline_image_size is None:
inline_image_size = '20%'
if ttl is None:
ttl = 'Fits for every Gene and Region'
if filename is None:
filename = 'fits'
if b_pathways:
create_pathway_index_html(data, fitter, fits, basedir, gene_dir, series_dir, use_correlations=use_correlations, b_unique=True)
create_pathway_index_html(data, fitter, fits, basedir, gene_dir, series_dir, use_correlations=use_correlations, b_unique=False)
n_ranks = 3 # actually we'll have ranks of 0 to n_ranks
flat_fits = {} # (gene,region) -> fit (may be None)
for g in gene_names:
for r in region_names:
flat_fits[(g,r)] = None
for dsfits in fits.itervalues():
for (g,r),fit in dsfits.iteritems():
if use_correlations:
score = fit.with_correlations.LOO_score
else:
score = fit.LOO_score
fit.score = score
fit.rank = int(np.ceil(n_ranks * score)) if score > 0 else 0
flat_fits[(g,r)] = fit
extra_fields_per_fit = list(enumerate(extra_fields_per_fit))
html = Template("""
<html>
<head>
<link rel="stylesheet" type="text/css" href="fits.css">
</head>
<body>
<H1>{{ttl}}</H1>
{% if b_R2_dist %}
<P>
<a href="{{scores_dir}}/scores.html">Distribution of LOO R2 scores</a>
</P>
{% endif %}
{% if b_pathways %}
<P>
<a href="pathway-fits-unique.html">Breakdown of fits for 17 pathways (unique)</a><br/>
<a href="pathway-fits.html">Breakdown of fits for 17 pathways (overlapping)</a>
</P>
{% endif %}
{% for href,txt in extra_top_links %}
<a href={{href}}>{{txt}}</a><br/>
{% endfor %}
{% if top_text %}
{{ top_text }}
{% endif %}
<P>
Column/row headings and/or cell entries may link to more details for the corresponding entity.
</P>
<P>
<table>
<th>
{% for column_name,dct_vals in extra_columns %}
<td class="tableExtraColumnHeading">
<b>{{column_name}}</b>
</td>
{% endfor %}
{% for region_name in region_names %}
<td class="tableHeading">
{% if link_to_correlation_plots %}
<a class=noColorChange href="{{correlations_dir}}/{{region_name}}.png"><b>{{region_name}}</b></a>
{% else %}
<b>{{region_name}}</b>
{% endif %}
</td>
{% endfor %}
</th>
{% for gene_name in gene_names %}
<tr>
<td>
<a href="{{gene_dir}}/{{gene_name}}.png"><b>{{gene_name}}</b></a>
</td>
{% for column_name,dct_vals in extra_columns %}
<td>
{{ '%.2g' | format(dct_vals[gene_name]) }}
</td>
{% endfor %}
{% for region_name in region_names %}
<td>
{% if flat_fits[(gene_name,region_name)] %}
<a class=noColorChange href="{{series_dir}}/fit-{{gene_name}}-{{region_name}}.png">
{% if flat_fits[(gene_name,region_name)].score %}
{% if b_inline_images %}
R2 =
{% endif %}
{% if show_R2 %}
<div class="score rank{{flat_fits[(gene_name,region_name)].rank}}">
{{flat_fits[(gene_name,region_name)].score | round(2)}}
</div>
{% endif %}
{% for i,f in extra_fields_per_fit %}
{% set txt,cls = f(flat_fits[(gene_name,region_name)]) %}
{% if i>0 or show_R2 %}
<br/>
{% endif %}
<div class="fitField {{cls}}">
<b>{{txt}}</b>
</div>
{% endfor %}
{% else %}
No Score
{% endif %}
{% if b_inline_images %}
<br/>
<img src="{{series_dir}}/fit-{{gene_name}}-{{region_name}}.png" height="{{inline_image_size}}">
{% endif %}
</a>
{% endif %}
</td>
{% endfor %}
</tr>
{% endfor %}
</table>
</P>
</body>
</html>
""").render(**locals())
filename = join(basedir,'{}.html'.format(filename))
print 'Saving HTML to {}'.format(filename)
with open(filename, 'w') as f:
f.write(html)
shutil.copy(join(resources_dir(),'fits.css'), basedir)
