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)
# ins_plot = fancplot.LinePlot(ins_dict, fill=False,
# colors={"gd7-nc14": "#648fff80", "Tollrm910-nc14": "#dc267f",
# "Toll10B-nc14": "#ffb00080", "3-4h": "#00000080"},
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)
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()
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