def uniqueCombosResponse(form):
# print "content-type: text/json\n"
tl = twolocus.TwoLocus("/csbiodata/public/www.csbio.unc.edu/htdocs/sgreens/pairwise_origins/")
strains = [[], []]
for set_num, set_id in enumerate(["background", "foreground"]):
for _, _, value, _ in helper.STRAIN_SETS:
new_strains = form.getvalue(value + set_id)
if type(new_strains) is list:
strains[set_num] += new_strains
elif new_strains is not None:
strains[set_num].append(new_strains)
# print '\n'.join(hex(line[0]) + ' ' + ' '.join(map(str, line[1:])) for line in tl.unique_combos(strains[0], strains[1]))
data = json.dumps(tl.unique_combos(strains[0], strains[1]), cls=helper.NumpyEncoder)
# with open('unique.json', "w+") as fp:
# with open('unique.json', "r") as fp:
# json.dump(tl.unique_combos(strains[0], strains[1]), fp, cls=helper.NumpyEncoder)
# data = json.load(fp)
# data = '0'
# panel = markup.page()
# panel.iframe(src='../sgreens/pairwise_origins/pairwiseGenome.html', chartWidth="100%", chartHeight="1000px")
# return panel
# print "content-type: text/html\n"
# with open('../sgreens/pairwise_origins/pairwiseGenome.html') as fp:
# print fp.read()<!DOCTYPE html>
helper.visualize_genome(data, tl)
def originsVisualizationResponse(form):
# print "content-type: text/json\n"
coarse_cutoff = 1e7
panel = markup.page()
plot_file = "ss_origins.html"
bokeh.plotting.output_file(plot_file)
tl = twolocus.TwoLocus("/csbiodata/public/www.csbio.unc.edu/htdocs/sgreens/pairwise_origins/")
strains = []
for _, _, value, _ in helper.STRAIN_SETS:
new_strains = form.getvalue(value)
if type(new_strains) is list:
strains += new_strains
elif new_strains is not None:
strains.append(new_strains)
data, colors = tl.pairwise_frequencies(strains)
absent_regions = tl.absent_regions(strains)
plot = bokeh.plotting.figure(
y_range=bokeh.models.Range1d(start=tl.offsets[-1] + 10e7, end=0),
height=750,
width=750,
background_fill_color="black",
tools=[
"tap",
"resize",
bokeh.models.HoverTool(names=["chroms"], tooltips=[("Proximal", "@proximal"), ("Distal", "@distal")]),
],
)
plot.axis.visible = False
plot.grid.grid_line_color = None
for combo_regions, color in zip(data, colors):
region_widths = np.subtract(combo_regions[1], combo_regions[0])
region_heights = np.subtract(combo_regions[3], combo_regions[2])
coarse_indices = np.logical_or(region_widths > coarse_cutoff, region_heights > coarse_cutoff)
region_widths = region_widths[coarse_indices]
region_heights = region_heights[coarse_indices]
x_positions = np.add(np.array(combo_regions[0])[coarse_indices], region_widths / 2)
y_positions = np.add(np.array(combo_regions[2])[coarse_indices], region_heights / 2)
plot.rect(
x_positions,
y_positions,
region_widths,
region_heights,
color="#" + hex(color)[2:].zfill(6),
fill_alpha=1.0 / len(strains),
line_alpha=0,
)
break
for combo_regions in absent_regions:
region_widths = np.subtract(combo_regions[1], combo_regions[0])
region_heights = np.subtract(combo_regions[3], combo_regions[2])
coarse_indices = np.logical_or(region_widths > coarse_cutoff, region_heights > coarse_cutoff)
region_widths = region_widths[coarse_indices]
region_heights = region_heights[coarse_indices]
x_positions = np.add(np.array(combo_regions[0])[coarse_indices], region_widths / 2)
y_positions = np.add(np.array(combo_regions[2])[coarse_indices], region_heights / 2)
plot.rect(x_positions, y_positions, region_widths, region_heights, color="white")
break
chrom_data = dict(x=[], y=[], width=[], height=[], proximal=[], distal=[])
for i in xrange(len(tl.sizes)):
for j in xrange(i, len(tl.sizes)):
chrom_data["x"].append(tl.offsets[i] + tl.sizes[i] / 2)
chrom_data["y"].append(tl.offsets[j] + tl.sizes[j] / 2)
chrom_data["width"].append(tl.sizes[i])
chrom_data["height"].append(tl.sizes[j])
chrom_data["proximal"].append(twolocus.INT_TO_CHROMO[i + 1])
chrom_data["distal"].append(twolocus.INT_TO_CHROMO[j + 1])
chrom_data_source = bokeh.models.ColumnDataSource(data=chrom_data)
plot.rect(
x="x",
y="y",
width="width",
height="height",
fill_alpha=0,
line_color="grey",
hover_alpha=0.5,
name="chroms",
source=chrom_data_source,
)
text_offsets = tl.offsets.copy()[:-1]
text_offsets[-3] += 5e7
plot.text(
x=-15e7,
y=[offset + 10e7 for offset in text_offsets],
text=twolocus.INT_TO_CHROMO[1:],
text_color="white",
text_font_size="10pt",
)
plot.text(
x=text_offsets,
y=tl.offsets[-1] + 10e7,
text=twolocus.INT_TO_CHROMO[1:],
text_color="white",
text_font_size="8pt",
)
inset_plot = bokeh.plotting.figure()
inset_plot.x_range.bounds = "auto"
inset_plot.y_range.bounds = "auto"
inset_data_source = bokeh.models.ColumnDataSource(data=dict(x=[], y=[], width=[], height=[]))
inset_plot.rect("x", "y", "width", "height", color="black")
bokeh.plotting.show(bokeh.io.hplot(plot, inset_plot))
with open(plot_file) as fp:
panel.add(fp.read())
return panel
helper.visualize_genome(data, tl, len(strains))
