def line(x_datas,
y_datas,
names=None,
colors=None,
xlim=(None, None),
ylim=(None, None),
**kwargs):
"""Create a simple line plot.
:param x_datas: a list of datasets, each item containing the
data for that set.
:params y_datas: a list of weight vectors (one for each dataset).
:param names: the name of each dataset.
:param colors: color used to plot each dataset.
:param xlim: tuple for plotting limits (start, end). A value None will
trigger calculation from the data.
:param ylim: tuple for plotting limits (start, end). A value None will
trigger calculation from the data.
:param kwargs: kwargs for bokeh figure.
:returns: a bokeh plot.
After creating this plot, you may wish to change the following:
* p.xaxis.axis_label
* p.yaxis.axis_label
"""
return simple(x_datas,
y_datas,
names=names,
colors=colors,
xlim=xlim,
ylim=ylim,
style='line',
**kwargs)
def dotplot_assembly(self, assembly_maf):
"""Dotplot the assembly."""
records = list()
with open(assembly_maf) as maf:
while True:
line = maf.readline()
print(line)
if line.startswith('#'):
continue
elif line.startswith('a'):
r1 = maf.readline().split()[1:5]
r2 = maf.readline().split()[1:5]
maf.readline()
records.append(r1 + r2)
elif line == "":
break
else:
print(line)
raise IOError("Cannot read alignment file")
names = [
'ref', 'rstart', 'rlen', 'rorient', 'query', 'qstart', 'qlen',
'qorient'
]
df = pd.DataFrame(records, columns=names)
df = df.loc[df['qorient'] == '+']
for f in ['qstart', 'qlen', 'rstart', 'rlen']:
df[f] = df[f].astype(int)
df['qend'] = df['qstart'] + df['qlen']
df['rend'] = df['rstart'] + df['rlen']
df['qend'] = df['qend'].astype(int)
df['rend'] = df['rend'].astype(int)
dotplot = base.simple([], [],
xlim=(0, max(df['rend'])),
ylim=(0, max(df['qend'])),
width=440,
height=400,
x_axis_label='position',
y_axis_label='position',
title=assembly_maf)
dotplot.segment(df['rstart'], df['qstart'], df['rend'], df['qend'])
return dotplot
def steps(x_datas,
y_datas,
names=None,
colors=None,
xlim=(None, None),
ylim=(None, None),
mode='before',
**kwargs):
"""Create a simple step-line plot.
:param x_datas: a list of datasets, each item containing the
data for that set.
:params y_datas: a list of weight vectors (one for each dataset).
:param names: the name of each dataset.
:param colors: color used to plot each dataset.
:param xlim: tuple for plotting limits (start, end). A value None will
trigger calculation from the data.
:param ylim: tuple for plotting limits (start, end). A value None will
trigger calculation from the data.
:param mode: one of 'before', 'center', 'after' indicating where the step
(change in y value) should be placed.
:param kwargs: kwargs for bokeh figure.
:returns: a bokeh plot.
After creating this plot, you may wish to change the following:
* p.xaxis.axis_label
* p.yaxis.axis_label
"""
return simple(x_datas,
y_datas,
names=names,
colors=colors,
xlim=xlim,
ylim=ylim,
mode=mode,
style='steps',
**kwargs)