def make_qualimap_plots(qmglobals=None, coverage_per_contig=None):
"""Make qualimap summary plots"""
retval = {
"fig": {"coverage_per_contig": None, "globals": None},
"file": {"coverage_per_contig": coverage_per_contig, "globals": qmglobals},
"uri": {"coverage_per_contig": data_uri(coverage_per_contig), "globals": data_uri(qmglobals)},
}
# Globals
if qmglobals is not None:
df_all = pd.read_csv(qmglobals)
df_all["Sample"] = df_all["Sample"].astype("str")
fig = figure(
y_range=[0, max(df_all["number of reads"])],
title="Mapping summary",
title_text_font_size="12pt",
plot_width=400,
plot_height=400,
x_range=sorted(list(set(df_all["Sample"]))),
)
mdotplot(
fig,
x="Sample",
size=10,
df=df_all,
alpha=0.5,
y=["number of reads", "number of mapped reads", "number of duplicated reads", "number of unique reads"],
)
xaxis(fig, axis_label="sample", major_label_orientation=np.pi / 3, axis_label_text_font_size="10pt")
yaxis(fig, axis_label="count", major_label_orientation=1, axis_label_text_font_size="10pt")
retval["fig"]["globals"] = fig
# Coverage per contig
if coverage_per_contig is not None:
df_all = pd.read_csv(coverage_per_contig, index_col=0)
df_all["Sample"] = df_all["Sample"].astype("str")
fig = figure(width=300, height=300)
points(
fig, x="chrlen_percent", y="mapped_bases_percent", df=df_all, glyph="text", text="chr", text_font_size="8pt"
)
main(fig, title_text_font_size="8pt")
xaxis(fig, axis_label="Chromosome length of total (%)", axis_label_text_font_size="8pt")
yaxis(fig, axis_label="Mapped bases of total (%)", axis_label_text_font_size="8pt")
gp = facet_grid(
fig,
x="chrlen_percent",
y="mapped_bases_percent",
df=df_all,
groups=["Sample"],
width=300,
height=300,
share_x_range=True,
share_y_range=True,
title_text_font_size="12pt",
)
for fig in [item for sublist in gp.children for item in sublist]:
abline(fig, x="chrlen_percent", y="mapped_bases_percent", df=df_all, slope=1)
retval["fig"]["coverage_per_contig"] = gp
return retval
def facet_grid_hist(self, **kwargs):
"""facet_grid hist wrapper.
Returns:
plist (list): list of bokeh plot objects
"""
kwargs.update(self.kw)
f = figure(**kwargs['figure'])
mlines(f, df=self, **kwargs['renderer'])
gp = facet_grid(f, df=self, ncol=self.ncol,
**kwargs['facet'])
plist = [x for sublist in gp.children for x in sublist]
return plist
def test_init_groups(self):
self._fig.line("x", "y", legend="y", source=self._source)
self._fig.line("x", "z", legend="z", source=self._source, color="red")
gp = facet_grid(self._fig, "x", ["y", "z"], self._data, groups=["sex"])
def test_init(self):
self._fig.circle("x", "y", source=self._source)
facet_grid(self._fig, "x", "y", source=self._source)
def test_init_groups(self):
self._fig.line("x", "y", legend="y", source=self._source)
self._fig.line("x", "z", legend="z", source=self._source, color="red")
gp = facet_grid(self._fig, "x", ["y", "z"], self._data, groups=["sex"])
def test_init(self):
self._fig.circle("x", "y", source=self._source)
facet_grid(self._fig, "x", "y", source=self._source)