def test_lineplot_dict_input(self, data_source, bin_size):
data = {k: getattr(self, d) for k, d in data_source.items()}
lplot = kplot.LinePlot(data, bin_size=bin_size)
gfig = kplot.GenomicFigure([lplot])
fig, axes = gfig.plot("chr11:77497000-77500000")
assert all(len(l.get_ydata()) > 5 for a in axes for l in a.get_lines())
assert all(l.get_label() == n_p
for l, n_p in zip(axes[0].get_lines(), data.keys()))
def test_lineplot(self, data_source, bin_size):
data = [getattr(self, d) for d in data_source]
if len(data) == 1:
data = data[0]
lplot = kplot.LinePlot(data, bin_size=bin_size)
gfig = kplot.GenomicFigure([lplot])
fig, axes = gfig.plot("chr11:77497000-77500000")
assert all(len(l.get_ydata()) > 5 for l in axes[0].get_lines())
def test_highlight_plot(self, crange):
bplot = kplot.BigWigPlot(self.bigwig_path)
gplot = kplot.GenePlot(self.gtf_path)
high = kplot.HighlightAnnotation(self.peak_path)
gfig = kplot.GenomicFigure([bplot, gplot, high])
fig, axes = gfig.plot("chr11:{}-{}".format(*crange))
p1 = high.patches[0]
assert gplot.ax.transAxes.transform(
(0,
0))[1] == pytest.approx(p1._transform.transform(p1.get_xy())[1])
def test_geneplot(self, collapse, squash_group):
squash, group_by = squash_group
gplot = kplot.GenePlot(self.gtf_path,
collapse=collapse,
squash=squash,
group_by=group_by)
gfig = kplot.GenomicFigure([gplot])
selector = "chr11:77490000-77500000"
fig, axes = gfig.plot(selector)
assert len(axes[0].patches) == (19 if squash else 49)
plt.close(fig)
def plot_region(name, region, promoter, rnaseq_ylim):
output_file = os.path.join("figures", "figure_stg10_panels", name + ".pdf")
logging.info("Working on %s", name)
logging.info("Will write output to %s", output_file)
control_v4c = fancplot.Virtual4CPlot(control_stg10_hic, viewpoint=promoter,
aspect=0.05, color="black",
draw_minor_ticks=False)
gd7_v4c = fancplot.Virtual4CPlot(gd7_stg10_hic, viewpoint=promoter,
aspect=0.05, color="#648fff",
draw_minor_ticks=False)
Tollrm910_v4c = fancplot.Virtual4CPlot(Tollrm910_stg10_hic, viewpoint=promoter,
aspect=0.05, color="#dc267f",
draw_minor_ticks=False)
Toll10B_v4c = fancplot.Virtual4CPlot(Toll10B_stg10_hic, viewpoint=promoter,
aspect=0.05, color="#ffb000",
draw_minor_ticks=False)
ha_plot = fancplot.HighlightAnnotation(bed=pybedtools.BedTool(re.sub(":|-", " ", promoter), from_string=True),
plot1=control_v4c, plot2=Toll10B_v4c,
plot_kwargs={"color": "gray"})
plots = [control_stg10_hic_plot,
gd7_stg10_hic_plot,
Tollrm910_stg10_hic_plot,
Toll10B_stg10_hic_plot,
control_v4c,
gd7_v4c,
Tollrm910_v4c,
Toll10B_v4c,
ha_plot,
rnaseq_plot_E04,
rnaseq_plot_E48,
genes_plot
]
with fancplot.GenomicFigure(plots, ticks_last=True) as gfig:
fig, axes = gfig.plot(region)
seaborn.despine(ax=axes[4], top=True, right=True)
seaborn.despine(ax=axes[5], top=True, right=True)
seaborn.despine(ax=axes[6], top=True, right=True)
seaborn.despine(ax=axes[7], top=True, right=True)
axes[4].set_ylim([0, 0.025])
axes[5].set_ylim([0, 0.025])
axes[6].set_ylim([0, 0.025])
axes[7].set_ylim([0, 0.025])
# RNA-seq axes
axes[8].set_ylim([0, rnaseq_ylim])
axes[9].set_ylim([0, rnaseq_ylim])
# seaborn.despine(ax=axes[4], bottom=True)
# seaborn.despine(ax=axes[5], bottom=True)
fig.savefig(output_file, bbox_inches='tight')
def test_invert_x_independent_x(self, crange):
offset = 150000
bplot = kplot.BigWigPlot(self.bigwig_path)
gplot = kplot.GenePlot(self.gtf_path)
gfig = kplot.GenomicFigure([bplot, gplot], invert_x=True)
fig, axes = gfig.plot("chr11:{}-{}".format(*crange))
ax_lim = axes[0].get_xlim()
assert (ax_lim[0] > ax_lim[1]
for ax_lim in (a.get_xlim() for a in axes))
bplot = kplot.BigWigPlot(self.bigwig_path, invert_x=True)
gplot = kplot.GenePlot(self.gtf_path)
gfig = kplot.GenomicFigure([bplot, gplot], independent_x=True)
fig, axes = gfig.plot([
"chr11:{}-{}".format(*crange),
"chr11:{}-{}".format(crange[0] + offset, crange[1] + offset)
])
ax_lim = [ax.get_xlim() for ax in axes]
abs_tol = 10000
assert ax_lim[0][0] == pytest.approx(crange[1], abs=abs_tol)
assert ax_lim[0][1] == pytest.approx(crange[0], abs=abs_tol)
assert ax_lim[1][0] == pytest.approx(crange[1] + offset, abs=abs_tol)
assert ax_lim[1][1] == pytest.approx(crange[0] + offset, abs=abs_tol)
def plot_region(name, region, promoter, rnaseq_ylim):
output_file = os.path.join("figures", "figure_4_panels", name + ".pdf")
logging.info("Working on %s", name)
logging.info("Will write output to %s", output_file)
gd7_v4c = fancplot.Virtual4CPlot(gd7_nc14_hic,
viewpoint=promoter,
aspect=0.05,
color="#648fff",
draw_minor_ticks=False)
Tollrm910_v4c = fancplot.Virtual4CPlot(Tollrm910_nc14_hic,
viewpoint=promoter,
aspect=0.05,
color="#dc267f",
draw_minor_ticks=False)
Toll10B_v4c = fancplot.Virtual4CPlot(Toll10B_nc14_hic,
viewpoint=promoter,
aspect=0.05,
color="#ffb000",
draw_minor_ticks=False)
ha_plot = fancplot.HighlightAnnotation(bed=pybedtools.BedTool(
re.sub(":|-", " ", promoter), from_string=True),
plot1=gd7_v4c,
plot2=Toll10B_v4c,
plot_kwargs={"color": "gray"})
plots = [
gd7_nc14_hic_plot, rnaseq_plot_gd7, h3k27ac_plot_gd7, gd7_enh_plot,
h3k27me3_plot_gd7, Tollrm910_nc14_hic_plot, rnaseq_plot_Tollrm910,
h3k27ac_plot_Tollrm910, Tollrm910_enh_plot, h3k27me3_plot_Tollrm910,
Toll10B_nc14_hic_plot, rnaseq_plot_toll10b, h3k27ac_plot_toll10b,
toll10b_enh_plot, h3k27me3_plot_toll10b, gd7_v4c, Tollrm910_v4c,
Toll10B_v4c, ha_plot, genes_plot
]
with fancplot.GenomicFigure(plots, ticks_last=True) as gfig:
fig, axes = gfig.plot(region)
seaborn.despine(ax=axes[15], top=True, right=True)
seaborn.despine(ax=axes[16], top=True, right=True)
seaborn.despine(ax=axes[17], top=True, right=True)
# axes[15].set_ylim([0, 0.02])
# axes[16].set_ylim([0, 0.02])
# axes[17].set_ylim([0, 0.02])
# RNA-seq axes
axes[1].set_ylim([0, rnaseq_ylim])
axes[6].set_ylim([0, rnaseq_ylim])
axes[11].set_ylim([0, rnaseq_ylim])
# seaborn.despine(ax=axes[4], bottom=True)
# seaborn.despine(ax=axes[5], bottom=True)
fig.savefig(output_file)
def test_hicplot2d_inputs(self, norm, colormap, colorbar, blend_zero,
aspect, vrange, crange, unmappable_color,
adjust_range):
start, end = crange
vmin, vmax = vrange
hplot = kplot.HicPlot2D(hic_data=self.hic_matrix,
title="quark",
norm=norm,
vmin=vmin,
vmax=vmax,
colormap=colormap,
show_colorbar=colorbar,
adjust_range=adjust_range,
blend_zero=blend_zero,
aspect=aspect,
unmappable_color=unmappable_color)
gfig = kplot.GenomicFigure([hplot])
selector = "chr11:{}-{}".format(start, end)
fig, axes = gfig.plot(selector)
assert axes[0].get_title() == "quark"
norm_values = {"lin": mpl.colors.Normalize, "log": mpl.colors.LogNorm}
assert isinstance(hplot.norm, norm_values[norm])
assert axes[0].get_xlim() == (start, end)
assert axes[0].get_ylim() == (start, end)
if vmin is not None:
assert hplot.im.norm.vmin == vmin
if vmax is not None:
assert hplot.im.norm.vmax == vmax
assert hplot.aspect == aspect
assert abs_ax_aspect(axes[0]) == pytest.approx(aspect)
colorbar_values = {True: mpl.colorbar.Colorbar, False: type(None)}
assert isinstance(hplot.colorbar, colorbar_values[colorbar])
hic_matrix = self.hic_matrix[selector, selector]
zero_mask = np.isclose(hic_matrix, 0.)
unmap_mask = np.all(zero_mask, axis=0)
unmap_mask = np.logical_or(unmap_mask, unmap_mask[:, np.newaxis])
if unmappable_color is not None:
unmap_color = mpl.colors.colorConverter.to_rgba(unmappable_color)
assert np.all(
np.isclose(hplot.im.get_array()[unmap_mask, :], unmap_color))
# blend zero only really makes sense with log normalization, with
# linear normalization 0 values map to the first colormap value anyway
if norm == "log":
exp_zero = np.logical_and(zero_mask, np.logical_not(unmap_mask))
if np.sum(exp_zero) > 0:
zero_value = hplot.colormap(0)
zero_blended = np.all(
np.isclose(hplot.im.get_array()[exp_zero, :], zero_value))
assert blend_zero == zero_blended
plt.close(fig)
def test_hicsliceplot(self, n_hic, yscale, ylim, slice_region, names):
hic_data = self.hic_matrix if n_hic == 1 else [self.hic_matrix] * n_hic
names_passed = None if names is None else [
"hic{}".format(i) for i in range(n_hic)
]
splot = kplot.HicSlicePlot(hic_data,
slice_region,
names=names_passed,
ylim=ylim,
yscale=yscale)
gfig = kplot.GenomicFigure([splot])
selector = "chr11:{}-{}".format(77400000, 78600000)
fig, axes = gfig.plot(selector)
assert axes[0].get_yscale() == yscale
for a, b in zip(ylim, axes[0].get_ylim()):
assert a is None or a == pytest.approx(b)
if names is not None:
assert all(l.get_label() == n_p
for l, n_p in zip(axes[0].get_lines(), names_passed))
plt.close(fig)
def test_tick_removal(self, width, cax_width, ticks_last, draw_labels,
draw_ticks, draw_x_axis):
splot = kplot.HicSlicePlot(self.hic_matrix, "chr11:77800000-77850000")
hplot = kplot.HicPlot2D(hic_data=self.hic_matrix,
draw_ticks=draw_ticks,
draw_tick_labels=draw_labels,
draw_x_axis=draw_x_axis)
hplot2 = kplot.HicPlot(hic_data=self.hic_matrix)
gfig = kplot.GenomicFigure([splot, hplot, hplot2],
width=width,
ticks_last=ticks_last,
cax_width=cax_width)
selector = "chr11:{}-{}".format(77400000, 78600000)
fig, axes = gfig.plot(selector)
# hplot2 should always have labels and lines
assert all(l.get_visible() for l in axes[2].get_xticklabels()) and all(
l.get_visible() for l in axes[2].xaxis.get_majorticklines())
# hplot labels are affected by the three draw parameters
should_have_labels = draw_x_axis and draw_labels and (not ticks_last)
assert should_have_labels == all(l.get_visible()
for l in axes[1].get_xticklabels())
# But it should have tick lines even when ticks_last=True
should_have_ticks = draw_x_axis and draw_ticks
assert should_have_ticks == all(
l.get_visible() for l in axes[1].xaxis.get_majorticklines())
assert should_have_ticks == all(
l.get_visible() for l in axes[1].xaxis.get_minorticklines())
# splot should always have ticks and lines
assert all(l.get_visible() for l in axes[0].xaxis.get_majorticklines())
assert all(l.get_visible() for l in axes[0].xaxis.get_minorticklines())
# splot only labels if ticks_last=False
assert ticks_last != all(l.get_visible()
for l in axes[0].get_xticklabels())
bbox = axes[0].get_position()
figsize = fig.get_size_inches()
assert bbox.width * figsize[0] == pytest.approx(width)
bbox = hplot.cax.get_position()
assert bbox.width * figsize[0] == pytest.approx(cax_width)
plt.close(fig)
def test_bigwig_plot(self, file, crange, n_bw, ylim, yscale, names,
bin_size):
path = getattr(self, "{}_path".format(file))
bw_data = path if n_bw == 1 else [path] * n_bw
names_passed = None if names is None else [
"bw{}".format(i) for i in range(n_bw)
]
bplot = kplot.BigWigPlot(bw_data,
names=names_passed,
bin_size=bin_size,
ylim=ylim,
yscale=yscale)
gfig = kplot.GenomicFigure([bplot])
fig, axes = gfig.plot("chr11:{}-{}".format(*crange))
assert axes[0].get_yscale() == yscale
for a, b in zip(ylim, axes[0].get_ylim()):
assert a is None or a == pytest.approx(b)
if names is not None:
assert all(l.get_label() == n_p
for l, n_p in zip(axes[0].get_lines(), names_passed))
# Should figure out exactly how many data points I expect instead...
assert all(len(l.get_ydata()) > 5 for l in axes[0].get_lines())
plt.close(fig)
def plot_region(name, region):
output_file = os.path.join("figures", "figure_4_panels", name + ".pdf")
logging.info("Working on %s", name)
logging.info("Will write output to %s", output_file)
gd7_nc14_hic = fanc.load(os.path.join("data", "hic", "merged", "gd7-nc14",
"hic", "gd7-nc14_5kb.hic"),
mode="r")
gd7_nc14_hic_plot = fancplot.HicPlot(gd7_nc14_hic,
norm="log",
vmin=1e-03,
vmax=1e-01,
draw_minor_ticks=False,
title="gd7",
max_dist='250kb')
gd7_nc14_diff = fanc.load(os.path.join(
"data", "hic", "merged", "gd7-nc14", "hic",
"diff_control-nc14_gd7-nc14_5kb.hic"),
mode="r")
gd7_nc14_diff_plot = fancplot.HicPlot(gd7_nc14_diff,
norm="lin",
colormap='bwr_r',
vmin=-0.01,
vmax=0.01,
draw_minor_ticks=False,
max_dist='250kb')
Tollrm910_nc14_hic = fanc.load(os.path.join("data", "hic", "merged",
"Tollrm910-nc14", "hic",
"Tollrm910-nc14_5kb.hic"),
mode="r")
Tollrm910_nc14_hic_plot = fancplot.HicPlot(Tollrm910_nc14_hic,
norm="log",
vmin=1e-03,
vmax=1e-01,
draw_minor_ticks=False,
title="Tollrm910",
max_dist='250kb')
Tollrm910_nc14_diff = fanc.load(os.path.join(
"data", "hic", "merged", "Tollrm910-nc14", "hic",
"diff_control-nc14_Tollrm910-nc14_5kb.hic"),
mode="r")
Tollrm910_nc14_diff_plot = fancplot.HicPlot(Tollrm910_nc14_diff,
norm="lin",
colormap='bwr_r',
vmin=-0.01,
vmax=0.01,
draw_minor_ticks=False,
max_dist='250kb')
Toll10B_nc14_hic = fanc.load(os.path.join("data", "hic", "merged",
"Toll10B-nc14", "hic",
"Toll10B-nc14_5kb.hic"),
mode="r")
Toll10B_nc14_hic_plot = fancplot.HicPlot(Toll10B_nc14_hic,
norm="log",
vmin=1e-03,
vmax=1e-01,
draw_minor_ticks=False,
title="Toll10B",
max_dist='250kb')
Toll10B_nc14_diff = fanc.load(os.path.join(
"data", "hic", "merged", "Toll10B-nc14", "hic",
"diff_control-nc14_Toll10B-nc14_5kb.hic"),
mode="r")
Toll10B_nc14_diff_plot = fancplot.HicPlot(Toll10B_nc14_diff,
norm="lin",
colormap='bwr_r',
vmin=-0.01,
vmax=0.01,
draw_minor_ticks=False,
max_dist='250kb')
genes = "external_data/flybase/dmel-all-r6.30.gtf.gz"
genes_plot = fancplot.GenePlot(genes,
squash=True,
group_by="gene_symbol",
aspect=0.15,
label_field="gene_symbol",
show_labels=False,
draw_minor_ticks=False)
rnaseq_dict = {
name:
os.path.join("external_data", "koenecke_2016_2017", "rnaseq_aligned",
name + "_sorted_filtered_merged_canonical_chrs_rnaseq.bw")
for name in ["gd7", "tlrm910", "tl10b"]
}
h3k27ac_dict = {
name: os.path.join(
"external_data", "koenecke_2016_2017", "chipseq_aligned",
"H3K27ac_" + name + "_sorted_filtered_merged_canonical_chrs.bw")
for name in ["gd7", "tl10b"]
}
h3k27ac_dict["Tollrm910"] = os.path.join(
"external_data", "extra_chip-seq", "chipseq_aligned",
"H3K27ac_Tollrm910_sorted_filtered_merged_canonical_chrs.bw")
h3k27me3_dict = {
name: os.path.join(
"external_data", "koenecke_2016_2017", "chipseq_aligned",
"H3K27me3_" + name + "_sorted_filtered_merged_canonical_chrs.bw")
for name in ["gd7", "tl10b"]
}
h3k27me3_dict["Tollrm910"] = os.path.join(
"external_data", "extra_chip-seq", "chipseq_aligned",
"H3K27me3_Tollrm910_sorted_filtered_merged_canonical_chrs.bw")
# ins_dict = {name: os.path.join("data", "boundaries", name + "_2kb_8.bw")
# for name in ["gd7-nc14", "Tollrm910-nc14", "Toll10B-nc14", "3-4h"]}
rnaseq_ylim = fancplot.helpers.LimitGroup()
rnaseq_ylim = [0, 10]
h3k27ac_ylim = fancplot.helpers.LimitGroup()
h3k27me3_ylim = fancplot.helpers.LimitGroup()
rnaseq_plot_gd7 = fancplot.LinePlot(rnaseq_dict['gd7'],
fill=False,
plot_kwargs={'color': "#648fff"},
draw_minor_ticks=False,
aspect=0.05,
ylim=rnaseq_ylim,
n_yticks=2)
h3k27ac_plot_gd7 = fancplot.LinePlot(h3k27ac_dict['gd7'],
fill=False,
plot_kwargs={'color': "#648fff"},
draw_minor_ticks=False,
aspect=0.05,
ylim=h3k27ac_ylim,
n_yticks=2)
h3k27me3_plot_gd7 = fancplot.LinePlot(h3k27me3_dict['gd7'],
fill=False,
plot_kwargs={'color': "#648fff"},
draw_minor_ticks=False,
aspect=0.05,
ylim=h3k27me3_ylim,
n_yticks=2)
rnaseq_plot_Tollrm910 = fancplot.LinePlot(rnaseq_dict['tlrm910'],
fill=False,
plot_kwargs={'color': "#dc267f"},
draw_minor_ticks=False,
aspect=0.05,
ylim=rnaseq_ylim,
n_yticks=2)
h3k27ac_plot_Tollrm910 = fancplot.LinePlot(
h3k27ac_dict['Tollrm910'],
fill=False,
plot_kwargs={'color': "#dc267f"},
draw_minor_ticks=False,
aspect=0.05,
ylim=h3k27ac_ylim,
n_yticks=2)
h3k27me3_plot_Tollrm910 = fancplot.LinePlot(
h3k27me3_dict['Tollrm910'],
fill=False,
plot_kwargs={'color': "#dc267f"},
draw_minor_ticks=False,
aspect=0.05,
ylim=h3k27me3_ylim,
n_yticks=2)
rnaseq_plot_toll10b = fancplot.LinePlot(rnaseq_dict['tl10b'],
fill=False,
plot_kwargs={'color': "#ffb000"},
draw_minor_ticks=False,
aspect=0.05,
ylim=rnaseq_ylim,
n_yticks=2)
h3k27ac_plot_toll10b = fancplot.LinePlot(h3k27ac_dict['tl10b'],
fill=False,
plot_kwargs={'color': "#ffb000"},
draw_minor_ticks=False,
aspect=0.05,
ylim=h3k27ac_ylim,
n_yticks=2)
h3k27me3_plot_toll10b = fancplot.LinePlot(h3k27me3_dict['tl10b'],
fill=False,
plot_kwargs={'color': "#ffb000"},
draw_minor_ticks=False,
aspect=0.05,
ylim=h3k27me3_ylim,
n_yticks=2)
gd7_enh = "data/supplementary_tables/gd7_candidate_enhancers.bed"
gd7_enh_plot = fancplot.GenomicFeaturePlot(gd7_enh,
aspect=0.02,
color="#648fff",
draw_minor_ticks=False)
Tollrm910_enh = "data/supplementary_tables/Tollrm910_candidate_enhancers.bed"
Tollrm910_enh_plot = fancplot.GenomicFeaturePlot(Tollrm910_enh,
aspect=0.02,
color="#dc267f",
draw_minor_ticks=False)
toll10b_enh = "data/supplementary_tables/Toll10B_candidate_enhancers.bed"
toll10b_enh_plot = fancplot.GenomicFeaturePlot(toll10b_enh,
aspect=0.02,
color="#ffb000",
draw_minor_ticks=False)
plots = [
gd7_nc14_hic_plot, gd7_nc14_diff_plot, rnaseq_plot_gd7,
h3k27ac_plot_gd7, gd7_enh_plot, h3k27me3_plot_gd7,
Tollrm910_nc14_hic_plot, Tollrm910_nc14_diff_plot,
rnaseq_plot_Tollrm910, h3k27ac_plot_Tollrm910, Tollrm910_enh_plot,
h3k27me3_plot_Tollrm910, Toll10B_nc14_hic_plot, Toll10B_nc14_diff_plot,
rnaseq_plot_toll10b, h3k27ac_plot_toll10b, toll10b_enh_plot,
h3k27me3_plot_toll10b, genes_plot
]
with fancplot.GenomicFigure(plots, ticks_last=True) as gfig:
fig, axes = gfig.plot(region)
fig.savefig(output_file)
boundaries = fanc.Boundaries.from_insulation_score(insulation,
window_size=1000000)
# end snippet boundaries run
# start snippet boundaries regions
for boundary in boundaries.regions:
score = boundary.score
# end snippet boundaries regions
# start snippet boundaries plot
ph = fancplot.TriangularMatrixPlot(hic_100kb,
max_dist=5000000,
vmin=0,
vmax=0.05)
pb = fancplot.BarPlot(boundaries)
f = fancplot.GenomicFigure([ph, pb])
fig, axes = f.plot('chr18:18mb-28mb')
# end snippet boundaries plot
fig.savefig("../docsrc/api/analyse/images/boundaries.png")
plt.close(fig)
# start snippet boundaries fp
min_score = 1.0
robust_boundaries = []
for boundary in boundaries.regions:
score = boundary.score
if score >= min_score:
robust_boundaries.append(boundary)
# end snippet boundaries fp
# start snippet boundaries minscore
def test_genomic_feature_score_plot(self, attribute):
gfsplot = kplot.GenomicFeatureScorePlot(self.peak_path,
attribute=attribute)
gfig = kplot.GenomicFigure([gfsplot])
fig, axes = gfig.plot("chr11:77497000-77500000")
assert len(axes[0].patches) == 2
def test_genomic_feature_plot(self):
gfplot = kplot.GenomicFeaturePlot(self.peak_path, label_field=8)
gfig = kplot.GenomicFigure([gfplot])
fig, axes = gfig.plot("chr11:77497000-77500000")
assert len(axes[0].patches) == 2
file_name="architecture/comparisons/esc_vs_cn.diff")
fc_esc_cn = fanc.FoldChangeMatrix.from_matrices(hic_esc, hic_cn, log_cmp=True,
file_name="architecture/comparisons/esc_vs_cn.fc")
# end snippet comparisons compare
# start snippet comparisons plot
p_esc = fancplot.TriangularMatrixPlot(hic_esc, vmin=0, vmax=0.05,
max_dist=400000)
p_cn = fancplot.TriangularMatrixPlot(hic_cn, vmin=0, vmax=0.05,
max_dist=400000)
p_diff = fancplot.TriangularMatrixPlot(diff_esc_cn, vmin=-0.02, vmax=0.02,
colormap='bwr', max_dist=400000)
p_fc = fancplot.TriangularMatrixPlot(fc_esc_cn, vmin=-1.5, vmax=1.5,
colormap='PiYG', max_dist=400000)
gf = fancplot.GenomicFigure([p_esc, p_cn, p_diff, p_fc], ticks_last=True)
fig, axes = gf.plot("chr1:167.9mb-168.7mb")
# end snippet comparisons plot
fig.savefig("../docsrc/api/analyse/images/comparisons_matrices.png")
plt.close(fig)
# start snippet comparisons custom
from fanc.architecture.comparisons import ComparisonMatrix
class CustomComparisonMatrix(ComparisonMatrix):
_classid = 'CUSTOMCOMPARISONMATRIX'
def __init__(self, *args, **kwargs):
ComparisonMatrix.__init__(self, *args, **kwargs)
def plot_regions(regions):
h = fanc.load(os.path.join("data", "hic", "merged", "3-4h", "hic",
"3-4h_2kb.hic"),
mode="r")
h_plot = fancplot.HicPlot(h,
vmin=1e-03,
vmax=1e-01,
norm="log",
draw_minor_ticks=False)
genes = "external_data/flybase/dmel-all-r6.30.gtf.gz"
genes_plot = fancplot.GenePlot(genes,
squash=True,
group_by="gene_symbol",
aspect=0.15,
label_field="gene_symbol",
show_labels=False,
draw_minor_ticks=False)
rnaseq_dict = {
name:
os.path.join("external_data", "koenecke_2016_2017", "rnaseq_aligned",
name + "_sorted_filtered_merged_canonical_chrs_rnaseq.bw")
for name in ["gd7", "tlrm910", "tl10b"]
}
h3k27ac_dict = {
name: os.path.join(
"external_data", "koenecke_2016_2017", "chipseq_aligned",
"H3K27ac_" + name + "_sorted_filtered_merged_canonical_chrs.bw")
for name in ["gd7", "tl10b"]
}
h3k27ac_dict["Tollrm910"] = os.path.join(
"external_data", "extra_chip-seq", "chipseq_aligned",
"H3K27ac_Tollrm910_sorted_filtered_merged_canonical_chrs.bw")
rnaseq_ylim = fancplot.helpers.LimitGroup()
h3k27ac_ylim = fancplot.helpers.LimitGroup()
polii_ylim = fancplot.helpers.LimitGroup()
# polii_chip_early = os.path.join("external_data", "blythe_2015", "aligned",
# "PolII-pSer5_NC14-early_sorted_filtered_merged_canonical_chrs.bw")
# polii_chip_mid = os.path.join("external_data", "blythe_2015", "aligned",
# "PolII-pSer5_NC14-middle_sorted_filtered_merged_canonical_chrs.bw")
polii_chip_late = os.path.join(
"external_data", "blythe_2015", "aligned",
"PolII-pSer5_NC14-late_sorted_filtered_merged_canonical_chrs.bw")
# polii_early_plot = fancplot.LinePlot(polii_chip_early, fill=True, plot_kwargs={'color': "black"},
# draw_minor_ticks=False, aspect=0.05,
# ylim=polii_ylim, n_yticks=2)
# polii_mid_plot = fancplot.LinePlot(polii_chip_mid, fill=True, plot_kwargs={'color': "black"},
# draw_minor_ticks=False, aspect=0.05,
# ylim=polii_ylim, n_yticks=2)
polii_late_plot = fancplot.LinePlot(polii_chip_late,
fill=True,
plot_kwargs={'color': "black"},
draw_minor_ticks=False,
aspect=0.05,
ylim=polii_ylim,
n_yticks=2)
rnaseq_plot_gd7 = fancplot.LinePlot(rnaseq_dict['gd7'],
fill=True,
plot_kwargs={'color': "#648fff"},
draw_minor_ticks=False,
aspect=0.05,
n_yticks=2)
h3k27ac_plot_gd7 = fancplot.LinePlot(h3k27ac_dict['gd7'],
fill=True,
plot_kwargs={'color': "#648fff"},
draw_minor_ticks=False,
aspect=0.05,
ylim=h3k27ac_ylim,
n_yticks=2)
rnaseq_plot_Tollrm910 = fancplot.LinePlot(rnaseq_dict['tlrm910'],
fill=True,
plot_kwargs={'color': "#dc267f"},
draw_minor_ticks=False,
aspect=0.05,
n_yticks=2)
h3k27ac_plot_Tollrm910 = fancplot.LinePlot(
h3k27ac_dict['Tollrm910'],
fill=True,
plot_kwargs={'color': "#dc267f"},
draw_minor_ticks=False,
aspect=0.05,
ylim=h3k27ac_ylim,
n_yticks=2)
rnaseq_plot_toll10b = fancplot.LinePlot(rnaseq_dict['tl10b'],
fill=True,
plot_kwargs={'color': "#ffb000"},
draw_minor_ticks=False,
aspect=0.05,
n_yticks=2)
h3k27ac_plot_toll10b = fancplot.LinePlot(h3k27ac_dict['tl10b'],
fill=True,
plot_kwargs={'color': "#ffb000"},
draw_minor_ticks=False,
aspect=0.05,
ylim=h3k27ac_ylim,
n_yticks=2)
gd7_enh = "data/supplementary_tables/gd7_candidate_enhancers.bed"
gd7_enh_plot = fancplot.GenomicFeaturePlot(gd7_enh,
aspect=0.02,
color="#648fff",
draw_minor_ticks=False)
Tollrm910_enh = "data/supplementary_tables/Tollrm910_candidate_enhancers.bed"
Tollrm910_enh_plot = fancplot.GenomicFeaturePlot(Tollrm910_enh,
aspect=0.02,
color="#dc267f",
draw_minor_ticks=False)
toll10b_enh = "data/supplementary_tables/Toll10B_candidate_enhancers.bed"
toll10b_enh_plot = fancplot.GenomicFeaturePlot(toll10b_enh,
aspect=0.02,
color="#ffb000",
draw_minor_ticks=False)
plots = [
h_plot,
# ins_plot,
# boundaries_plot,
genes_plot,
# hk_plot,
# polii_early_plot, polii_mid_plot,
polii_late_plot,
rnaseq_plot_gd7,
rnaseq_plot_Tollrm910,
rnaseq_plot_toll10b,
h3k27ac_plot_gd7,
h3k27ac_plot_Tollrm910,
h3k27ac_plot_toll10b,
gd7_enh_plot,
Tollrm910_enh_plot,
toll10b_enh_plot
]
with PdfPages(output_file) as pdf:
with fancplot.GenomicFigure(plots, ticks_last=True) as gfig:
for name, region, rnaseq_ylim in regions:
logging.info(region)
fig, axes = gfig.plot(region)
axes[3].set_ylim([0, rnaseq_ylim])
axes[4].set_ylim([0, rnaseq_ylim])
axes[5].set_ylim([0, rnaseq_ylim])
pdf.savefig()
# Donut O/E values
p_oe_d = fancplot.TriangularMatrixPlot(loop_info,
vmin=0,
vmax=4,
weight_field='oe_d',
colormap='Reds',
max_dist=600000)
# Donut FDR values
p_fdr_d = fancplot.TriangularMatrixPlot(loop_info,
vmin=0,
vmax=0.1,
weight_field='fdr_d',
colormap='binary_r',
max_dist=600000)
gf = fancplot.GenomicFigure([p_hic, p_oe_d, p_fdr_d], ticks_last=True)
fig, axes = gf.plot('chr11:77.4mb-78.6mb')
# end snippet loops matrix
fig.savefig("../docsrc/api/analyse/images/loops_annotate.png")
plt.close(fig)
# start snippet loops filters
# filter on O/E
enrichment_filter = fanc.peaks.EnrichmentPeakFilter(enrichment_ll_cutoff=1.75,
enrichment_d_cutoff=3,
enrichment_h_cutoff=2,
enrichment_v_cutoff=2)
loop_info.filter(enrichment_filter, queue=True)
# filter on FDR
fdr_filter = fanc.peaks.FdrPeakFilter(fdr_ll_cutoff=0.05,
