def wasabiplot(bam_filename, chrom, start, stop, strand, log_base=10,
color='steelblue', bad_cigar=INSERTION_DELETIONS,
coverage_cigar=COVERAGE_CIGAR, junction_cigar=JUNCTION_CIGAR,
ax=None, coverage_kws=None, curve_height_multiplier=0.2,
text_kws=TEXT_KWS, patch_kws=PATCH_KWS, warn_skipped=True,
annotate=True, **kwargs):
"""Get the number of reads that matched to the reference sequence
Parameters
----------
bam_filename : str
Name of the bam filename for logging purposes
chrom : str
Name of the reference chromosome
start, stop : int
Genome-based locations of the start and stop regions
strand : '+' | '-'
Strand to query
log_base : number or None, optional
The base to use for log-scaling the data. e.g. 10 would have log10 data
If None, the data is not log-scaled. (default=10)
color : valid matplotlib color
Color to use for both the coverage and junction plotting
allowed_cigar : tuple of str, optional
Which CIGAR string flags are allowed. (default=('M') aka match)
bad_cigar : tuple of str, optional
Which CIGAR string flags are not allowed. (default=('I', 'D') aka
insertion and deletion)
"""
if isinstance(bam_filename, pd.Series):
bam_filename = bam_filename.iloc[0]
plotter = WasabiPlotter(bam_filename, chrom, start, stop, strand, log_base,
color, bad_cigar, coverage_cigar, junction_cigar,
warn_skipped)
if ax is None:
ax = plt.gca()
coverage_kws = {} if coverage_kws is None else coverage_kws
coverage_kws.update(kwargs)
plotter.plot_coverage(color, ax, **coverage_kws)
plotter.plot_junctions(ax, curve_height_multiplier=curve_height_multiplier,
text_kws=text_kws, patch_kws=patch_kws,
annotate=annotate)
# Remove bottom spine
sns.despine(ax=ax, bottom=True)
# Add a zero-axis line
ax.hlines(0, 0, plotter.length, linewidth=0.5, zorder=-1)
if ax.is_last_row():
xticks = [int(x + start) for x in ax.get_xticks()]
ax.set(xticklabels=xticks)
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