def plot_n_ovlps_per_read(reads: List[TRRead],
overlaps: List[Overlap]):
n_ovlps_per_read = Counter()
for o in overlaps:
n_ovlps_per_read[o.a_read_id] += 1
n_ovlps_per_read[o.b_read_id] += 1
show_plot(make_hist([n_ovlps_per_read[read.id] for read in reads],
bin_size=1),
make_layout(x_title="# of overlaps per read",
y_title="Frequency",
x_range=(0, None)))
def plot_ulen_transition(read: TRRead):
"""Show positional distribution of unit lengths in `read."""
assert len(read.units) > 0, "No units to show"
show_plot(
make_scatter(**dict(
zip(('x', 'y'),
zip(*[
x for unit in read.units
for x in [(unit.start,
unit.length), (unit.end,
unit.length), (None, None)]
]))),
mode="lines+markers"),
make_layout(title=f"Read {read.id} (strand={read.strand})",
x_title="Start position",
y_title="Unit length [bp]",
x_range=(0, read.length)))
def plot_ulen_dist(reads: List[TRRead],
by: str = "total",
min_ulen: int = 1,
max_ulen: Optional[int] = None,
log_scale: bool = False):
"""Show a distribution of unit lengths in `reads`.
positional arguments:
@ reads : A list of TRRead objects.
optional arguments:
@ by : Must be one of {"total", "count"}.
@ [min|max]_ulen : Range of unit length to count.
"""
assert by in ("total", "count"), "`by` must be 'total' or 'count'"
ulens = [unit.length for read in reads for unit in read.units]
max_ulen = max(ulens) if max_ulen is None else max_ulen
ulen_counts = Counter(
list(filter(lambda x: min_ulen <= x <= max_ulen, ulens)))
if by == "total":
ulen_counts = {
ulen: ulen * count
for ulen, count in ulen_counts.items()
}
layout = make_layout(
width=1000,
height=500,
title=("Total bases for each unit length"
if by == "total" else "Number of units for each unit length"),
x_title="Unit length [bp]",
y_title=("Total bases [bp]" if by == "total" else "Frequency"),
x_range=(min_ulen, max_ulen))
if log_scale:
layout["yaxis_type"] = "log"
show_plot([
make_scatter(**dict(zip(
('x', 'y'), zip(*sorted(ulen_counts.items())))),
mode="lines",
name="Line graph<br>(for zooming out)",
show_legend=True),
make_hist(ulen_counts,
name="Bar graph<br>(for zooming in)",
show_legend=True)
],
layout=layout)
def plot_overlaps_for_read(read_id: int,
overlaps: List[Overlap],
min_ovlp_len: int = 10000):
_overlaps = list(filter(None, [o if o.a_read_id == read_id
else o.swap() if o.b_read_id == read_id
else None
for o in overlaps]))
assert len(_overlaps) > 0, "No overlaps for the read"
read_len = _overlaps[0].a_len
lens = [o.length for o in _overlaps]
diffs = [o.diff * 100 for o in _overlaps]
show_plot(make_scatter(x=lens,
y=diffs,
col=[o.b_read_id for o in _overlaps],
marker_size=8),
make_layout(
shapes=[make_line(min_ovlp_len,
min(diffs),
min_ovlp_len,
max(diffs),
col="red"), # min ovlp len threshold
make_line(read_len,
min(diffs),
read_len,
max(diffs),
col="green"), # read length (contained)
make_rect(min_ovlp_len,
min(diffs),
read_len,
max(diffs),
opacity=0.1), # accepted ovlps
make_line(lens[np.argmin(diffs)],
min(diffs),
lens[np.argmin(diffs)],
max(diffs)), # ovlp len of min diff
make_line(min(lens),
min(diffs),
max(lens),
min(diffs))])) # min ovlp diff
def plot_start_end(read_id: int,
overlaps: List[Overlap]):
# Convert overlaps so that a_read_id == read_id
_overlaps = list(filter(None, [o if o.a_read_id == read_id
else o.swap() if o.b_read_id == read_id
else None
for o in overlaps]))
assert len(_overlaps) > 0, "No overlaps for the read"
read_len = _overlaps[0].a_len
x, y, t, c = zip(*[
(o.a_start,
o.a_end,
f"read {o.b_read_id}<br>({o.b_start}, {o.b_end})<br>{o.type}",
o.b_read_id)
for o in _overlaps])
show_plot(make_scatter(x, y, text=t, col=c),
make_layout(width=700,
height=700,
x_title="Start",
y_title="End",
x_range=(-read_len * 0.05, read_len),
y_range=(0, read_len * 1.05)))
def plot_self(read: TRRead, unit_dist_by: str, max_dist: Optional[float],
max_slope_dev: float, plot_size: int):
if unit_dist_by == "repr":
assert read.repr_units is not None, "No representative units"
read_shapes = [
make_line(0, 0, read.length, read.length, width=2, col="grey")
]
tr_traces, tr_shapes = read_to_tr_obj(read, max_slope_dev)
unit_traces, unit_shapes = read_to_unit_obj(read, unit_dist_by, max_dist)
traces = tr_traces + unit_traces
shapes = read_shapes + tr_shapes + unit_shapes
layout = make_layout(plot_size,
plot_size,
title=f"Read {read.id} (strand={read.strand})",
x_range=(0, read.length),
y_range=(0, read.length),
x_grid=False,
y_grid=False,
y_reversed=True,
margin=dict(l=10, r=10, t=50, b=10),
shapes=shapes)
layout["yaxis"]["scaleanchor"] = "x"
show_plot(traces, layout)
def plot_ulen_composition(reads: Union[TRRead, List[TRRead]],
by: str = "total"):
"""Show composition of unit lengths in each of `reads`.
positional arguments:
@ reads : TRRead object of a list of TRRead objects.
optional arguments:
@ by : Must be one of {"total", "count"}.
"""
assert by in ("total", "count"), "`by` must be 'total' or 'count'"
if isinstance(reads, TRRead):
reads = [reads]
for read in reads:
assert len(read.units) > 0, f"Read {read.id}: no units to show"
comps = {
read.id: sorted(Counter([unit.length for unit in read.units]).items())
for read in reads
}
if by == "total":
comps = {
read_id: [(ulen, ulen * count) for ulen, count in counts]
for read_id, counts in comps.items()
}
show_plot(
[
make_scatter(**dict(zip(('x', 'y'), zip(*comps[read.id]))),
mode="lines+markers",
marker_size=6,
name=f"Read {read.id}",
show_legend=True) for read in reads
],
make_layout(
title="Composition of unit lengths",
x_title="Unit length [bp]",
y_title=("Total bases [bp]" if by == "total" else "Frequency")))
def plot_vs(a_read: TRRead, b_read: TRRead, unit_dist_by: str,
max_dist: Optional[float], plot_size: int):
assert a_read.synchronized and b_read.synchronized, \
"Both reads must be synchronized"
axis_traces, axis_shapes = reads_to_axis_obj(a_read, b_read)
matrix_traces, matrix_shapes = reads_to_matrix_obj(a_read, b_read,
unit_dist_by, max_dist)
traces = axis_traces + matrix_traces
shapes = axis_shapes + matrix_shapes
layout = make_layout(plot_size,
plot_size,
x_title=f"Read {a_read.id} (strand={a_read.strand})",
y_title=f"Read {b_read.id} (strand={b_read.strand})",
x_range=(-a_read.length * 0.05, a_read.length),
y_range=(0, b_read.length),
x_grid=False,
y_grid=False,
y_reversed=True,
x_zeroline=False,
y_zeroline=False,
margin=dict(l=10, r=10, t=50, b=10),
shapes=shapes)
layout["yaxis"]["scaleanchor"] = "x"
show_plot(traces, layout)
def draw_string_graph(sg: ig.Graph,
reads: Optional[Union[List[TRRead],
Dict[int, TRRead]]] = None,
kk_maxiter: int = 100000,
node_size: int = 8,
edge_width_per_bp: int = 5000,
plot_size: int = 900):
def v_to_read_id(v: ig.Vertex) -> int:
return int(v["name"].split(':')[0])
def cov_rate(read: TRRead) -> float:
return sum([unit.length for unit in read.units]) / read.length * 100
# [(source, target)], index == v.index
coords = sg.layout_kamada_kawai(maxiter=kk_maxiter)
traces = []
# Edge traces (multiple edges are red)
n_edges = Counter([(e.source, e.target) for e in sg.es])
e_to_headwidth_col = {
e: (max(e["length"] // edge_width_per_bp,
3), "black" if n_edges[(e.source, e.target)] == 1 else "red")
for e in sg.es
}
# Create Trace object for each unique pair of width and color
for col in ("black", "red"):
traces.append(
make_lines([(*coords[e.source], *coords[e.target])
for e in sg.es if e_to_headwidth_col[e][1] == col],
width=1,
col=col))
for width, col in set(e_to_headwidth_col.values()):
traces.append(
make_lines(
[((0.3 * coords[e.source][0] + 0.7 * coords[e.target][0]),
(0.3 * coords[e.source][1] + 0.7 * coords[e.target][1]),
*coords[e.target])
for e in sg.es if e_to_headwidth_col[e] == (width, col)],
width=width,
col=col))
edge_info = defaultdict(list)
for e in sg.es:
edge_info[(e.source, e.target)].append(
f"{e['length']} bp, {e['diff'] * 100:.2f}% diff" if "diff" in
e.attributes() else f"{e['length']} bp")
x, y, t, c = zip(*[((coords[e.source][0] + coords[e.target][0]) / 2,
(coords[e.source][1] + coords[e.target][1]) / 2,
f"{'<br>'.join(edge_info[(e.source, e.target)])}",
e_to_headwidth_col[e][1]) for e in sg.es])
traces.append(make_scatter(x=x, y=y, text=t, col=c, marker_size=1))
# Node trace with color by cover rate by TR units
if reads is not None:
reads_by_id = (reads if isinstance(reads, dict) else
{read.id: read
for read in reads})
cov_rates = [
cov_rate(reads_by_id[v_to_read_id(v)]) if reads is not None else 0.
for v in sg.vs
]
x, y, t = zip(*[(*coords[v.index],
f"{v['name']}<br>{cov_rates[v.index]:.1f}% covered")
for v in sg.vs])
traces.append(
make_scatter(x=x,
y=y,
text=t,
col=cov_rates,
col_range=(50, 100),
col_scale='YlGnBu',
show_scale=False,
marker_size=node_size,
marker_width=node_size / 5))
show_plot(
traces,
make_layout(width=plot_size,
height=plot_size,
x_grid=False,
y_grid=False,
x_zeroline=False,
y_zeroline=False,
x_show_tick_labels=False,
y_show_tick_labels=False,
margin=dict(l=0, r=0, b=0, t=0)))
def adaptive_filter_overlaps(overlaps: List[Overlap],
min_n_ovlp: int,
default_min_ovlp_len: int,
limit_min_ovlp_len: int,
filter_by_diff: bool = True,
plot: bool = False) -> List[Overlap]:
"""Filter overlaps by length and sequence dissimilarity by adaptively
changing the thresholds for individual read, considering the number of
overlaps at prefix and suffix of each read.
"""
# TODO: what is the difference with "best-N-overlaps" strategy?
def _filter_overlaps(_overlaps: List[Overlap]) -> List[Overlap]:
"""Filter overlaps with adaptive threshold of minimum overlap length
ranging [`limit_min_ovlp_len`, `default_min_ovlp_len`]."""
if len(_overlaps) == 0:
return _overlaps
olens = [o.length for o in _overlaps]
min_len = max(
min((min(olens) if len(_overlaps) < min_n_ovlp else sorted(
olens, reverse=True)[min_n_ovlp - 1]), default_min_ovlp_len),
limit_min_ovlp_len)
min_lens.append(min_len)
return list(filter(lambda o: o.length >= min_len, _overlaps))
overlaps_per_read = defaultdict(list)
for o in overlaps:
overlaps_per_read[o.a_read_id].append(o)
overlaps_per_read[o.b_read_id].append(o.swap())
filtered_overlaps = []
min_lens, max_diffs = [], [] # for plot
for read_id, _overlaps in overlaps_per_read.items():
# Filter overlaps with adaptive min overlap length threshold
# NOTE: contained overlaps are counted twice in pre and suf
pre_overlaps = _filter_overlaps(
list(filter(lambda o: o.a_start == 0, _overlaps)))
suf_overlaps = _filter_overlaps(
list(filter(lambda o: o.a_end == o.a_len, _overlaps)))
contains_overlaps = list(
filter(
lambda o:
(o.type == "contains" and o.length >= default_min_ovlp_len),
_overlaps))
_overlaps = sorted(set(pre_overlaps + suf_overlaps +
contains_overlaps))
if filter_by_diff and len(_overlaps) >= 2:
# Filter overlaps with adaptive overlap seq diff threshold
# NOTE: this is in order to exclude false contained overlaps
diffs = [o.diff for o in _overlaps]
max_diff = mean(diffs) + stdev(diffs) # TODO: rationale?
max_diffs.append(max_diff * 100)
_overlaps = list(filter(lambda o: o.diff <= max_diff, _overlaps))
filtered_overlaps += _overlaps
# Merge overlaps and remove duplicated overlaps
filtered_overlaps = sorted(
set([
o if o.a_read_id < o.b_read_id else o.swap()
for o in filtered_overlaps
]))
logger.info(f"{len(overlaps)} -> {len(filtered_overlaps)} overlaps")
if plot:
show_plot(
make_hist(min_lens, bin_size=500),
make_layout(x_title="Min overlap length at boundaries [bp]",
y_title="Frequency"))
if filter_by_diff:
show_plot(
make_hist(max_diffs, bin_size=0.1),
make_layout(x_title="Max sequence dissimilarity per read [%]",
y_title="Frequency"))
return filtered_overlaps
def plot_cigar(mappings: List[ContigMapping],
mutation_locations: List[int],
read_length: int,
true_fname: str,
line_width: int = 1):
"""Show alignments between contigs and the true sequence and also mutations.
positional arguments:
@ contig_cigars : Cigar and true start position for each contig.
@ mutation_locations : Positions of mutations in the true sequence.
optional arguments:
@ line_width : Width of the alignments in the plot.
"""
def make_lines_for_contigs() -> Tuple[List[go.Scatter], int]:
# Make line objects representing alignment paths
match_lines, nonmatch_lines, gap_lines = [], [], []
contig_start = 0
for i in range(len(mappings)):
if i > 0:
gap_lines.append((mappings[i - 1].end, contig_start,
mappings[i].start, contig_start))
_match_lines, _nonmatch_lines, contig_start = \
make_lines_for_contig(mappings[i], contig_start)
match_lines += _match_lines
nonmatch_lines += _nonmatch_lines
return ([
make_lines(match_lines, width=line_width),
make_lines(nonmatch_lines, width=line_width, col="red"),
make_lines(gap_lines, width=line_width, col="yellow")
], contig_start)
def make_lines_for_contig(
mapping: ContigMapping,
contig_start: int) -> List[Tuple[int, int, int, int]]:
match_lines, nonmatch_lines = [], []
contig_pos, true_pos = contig_start, mapping.start
for length, op in mapping.cigar:
if op in ('=', 'X'):
(match_lines if op == '=' else nonmatch_lines) \
.append((true_pos,
contig_pos,
true_pos + length,
contig_pos + length))
contig_pos += length
true_pos += length
elif op == 'I':
nonmatch_lines.append(
(true_pos, contig_pos, true_pos, contig_pos + length))
contig_pos += length
else:
nonmatch_lines.append(
(true_pos, contig_pos, true_pos + length, contig_pos))
true_pos += length
assert true_pos == mapping.end, "Invalid CIGAR"
return match_lines, nonmatch_lines, contig_pos
def make_dots_for_mutation_status():
nonlocal read_length, mutation_locations
# Remove boundary regions
mutation_locations = [pos - read_length for pos in mutation_locations]
# Check if the mutation is assembled for each mutation
mutation_status = {pos: None for pos in mutation_locations}
for mapping in mappings:
true_pos = mapping.start
for op in mapping.cigar.flatten():
if (true_pos in mutation_status
and mutation_status[true_pos] in (None, '=')):
mutation_status[true_pos] = op
# TODO: see bases around the mutation
if op != 'I':
true_pos += 1
return make_scatter(
x=mutation_locations,
y=[0] * len(mutation_locations),
col=[
'black' if mutation_status[pos] == '=' else 'red'
for pos in mutation_locations
],
marker_size=3)
mappings = sorted(mappings, key=lambda x: x.start)
traces_aln, contigs_length = make_lines_for_contigs()
trace_mutation = make_dots_for_mutation_status()
true_seq_length = load_fasta(true_fname)[0].length - 2 * read_length
show_plot(
traces_aln + [trace_mutation],
make_layout(width=800,
height=800 * contigs_length / true_seq_length,
x_title="True sequence",
y_title="Contig",
x_range=(0, true_seq_length),
y_range=(0, contigs_length),
x_grid=False,
y_grid=False,
x_zeroline=False,
y_zeroline=False,
y_reversed=True,
anchor_axes=True,
margin=dict(l=10, r=10, t=50, b=10)))