def plot_ref_genome(ref_placements,cycle,total_length,segSeqD,imputed_status,label_segs,onco_set=set()):
font0 = FontProperties()
rot_sp = global_rot/360.*total_length
for ind,refObj in ref_placements.iteritems():
seg_coord_tup = segSeqD[cycle[ind][0]]
# print(refObj.to_string())
start_angle, end_angle = start_end_angle(refObj.abs_end_pos,refObj.abs_start_pos,total_length)
# print start_angle,end_angle
#makes the reference genome wedges
patches.append(mpatches.Wedge((0,0), outer_bar, end_angle, start_angle, width=bar_width))
chrom = segSeqD[cycle[ind][0]][0]
f_color_v.append(chromosome_colors[chrom])
e_color_v.append('grey')
lw_v.append(0.2)
#makes the ticks on the reference genome wedges
if cycle[ind][1] == "+":
# posns = zip(range(seg_coord_tup[1],seg_coord_tup[2]+1),np.arange(refObj.abs_end_pos,refObj.abs_start_pos,-1))
posns = zip(range(seg_coord_tup[1],seg_coord_tup[2]+1),np.arange(refObj.abs_start_pos,refObj.abs_end_pos))
else:
# posns = zip(np.arange(seg_coord_tup[2],seg_coord_tup[1]-1,-1),np.arange(refObj.abs_end_pos,refObj.abs_start_pos,-1))
posns = zip(np.arange(seg_coord_tup[2],seg_coord_tup[1]-1,-1),np.arange(refObj.abs_start_pos,refObj.abs_end_pos))
tick_freq = max(30000,30000*int(np.floor(total_length/1000000)))
if refObj.abs_end_pos-refObj.abs_start_pos < 30000:
tick_freq = 10000
for j in posns:
if j[0] % tick_freq == 0:
text_angle = j[1]/total_length*360
x,y = pol2cart(outer_bar,(text_angle/360*2*np.pi))
x_t,y_t = pol2cart(outer_bar + 0.2,(text_angle/360*2*np.pi))
ax.plot([x,x_t],[y,y_t],color='grey',linewidth=1)
text_angle,ha = vu.correct_text_angle(text_angle)
txt = " " + str(int(round((j[0])/10000))) if ha == "left" else str(int(round((j[0])/10000))) + " "
ax.text(x_t,y_t,txt,color='grey',rotation=text_angle,
ha=ha,va="center",fontsize=9,rotation_mode='anchor')
gene_tree = vu.parse_genes(seg_coord_tup[0],args.ref)
relGenes = vu.rel_genes(gene_tree,seg_coord_tup,copy.copy(onco_set))
#plot the gene track
plot_gene_track(refObj.abs_start_pos,relGenes,seg_coord_tup,total_length,cycle[ind][1])
#label the segments by number in cycle
mid_sp = (refObj.abs_end_pos + refObj.abs_start_pos)/2
text_angle = mid_sp/total_length*360.
x,y = pol2cart((outer_bar-2*bar_width),(text_angle/360.*2.*np.pi))
font = font0.copy()
if imputed_status[ind]:
font.set_style('italic')
# font.set_weight('bold')
text_angle,ha = vu.correct_text_angle(text_angle)
if label_segs:
ax.text(x,y,cycle[ind][0]+cycle[ind][1],color='grey',rotation=text_angle,
ha=ha,fontsize=5,fontproperties=font,rotation_mode='anchor')
def plot_cmap_track(seg_placements, total_length, unadj_bar_height, color, seg_id_labels=False):
cycle_label_locs = defaultdict(list)
for ind, segObj in seg_placements.items():
bar_height = unadj_bar_height + segObj.track_height_shift
print("cmap_plot", segObj.id)
start_angle, end_angle = start_end_angle(segObj.abs_end_pos, segObj.abs_start_pos, total_length)
patches.append(mpatches.Wedge((0, 0), bar_height + bar_width, end_angle, start_angle, width=bar_width))
f_color_v.append(color)
e_color_v.append('k')
lw_v.append(0)
linewidth = min(0.25 * 2000000 / total_length, 0.25)
for i in segObj.label_posns:
if i > segObj.abs_end_pos or i < segObj.abs_start_pos:
continue
label_rads = i / total_length * 2 * np.pi
x, y = vu.pol2cart(bar_height, label_rads)
x_t, y_t = vu.pol2cart(bar_height + bar_width, label_rads)
# linewidth = min(0.2*2000000/total_length,0.2)
ax.plot([x, x_t], [y, y_t], color='k', alpha=0.9, linewidth=linewidth)
if seg_id_labels:
mid_sp = (segObj.abs_end_pos + segObj.abs_start_pos) / 2
text_angle = mid_sp / total_length * 360.
x, y = vu.pol2cart(bar_height - 1.2, (text_angle / 360. * 2. * np.pi))
text_angle, ha = vu.correct_text_angle(text_angle)
text = segObj.id + segObj.direction
ax.text(x, y, text, color='grey', rotation=text_angle,
ha=ha, fontsize=5, rotation_mode='anchor')
return cycle_label_locs
def plot_gene_track(currStart, relGenes, pTup, total_length, strand):
for ind,i in enumerate(relGenes):
truncStart = False
truncEnd = False
#e_posns is a list of tuples of exon (start,end)
#these can be plotted similarly to how the coding region is marked
tstart,tend,e_posns = relGenes[i]
seg_len = pTup[2] - pTup[1]
if strand == "+":
normStart = currStart + max(0,tstart-pTup[1])
normEnd = currStart + min(seg_len,tend-pTup[1])
else:
normEnd = currStart + min(seg_len,pTup[2]-tstart)
normStart = currStart + max(0,pTup[2] - tend)
# print max(0,tstart-pTup[1]),min(seg_len,tend-pTup[1]),seg_len
# print i,normStart,normEnd, currStart, currStart+seg_len,tstart,tend,strand
start_angle = normStart/total_length*360
end_angle = normEnd/total_length*360
text_angle = (start_angle + end_angle)/2.0
gene_to_locations[i].append((start_angle/360.,end_angle/360.))
if end_angle < 0 and start_angle > 0:
end_angle+=360
patches.append(mpatches.Wedge((0,0), outer_bar, start_angle, end_angle, width=bar_width/2.0))
f_color_v.append('k')
e_color_v.append('k')
lw_v.append(0)
# x,y = pol2cart(outer_bar+(bar_width/2.0),(text_angle/360*2*np.pi))
x_t,y_t = pol2cart(outer_bar + bar_width + 2,(text_angle/360*2*np.pi))
#ax.plot([x,x_t],[y,y_t],color='grey',linewidth=0.4)
text_angle,ha = vu.correct_text_angle(text_angle)
ax.text(x_t,y_t,i,color='k',rotation=text_angle,ha=ha,va="center",fontsize=9,rotation_mode='anchor')
for exon in e_posns:
if exon[1] > pTup[1] and exon[0] < pTup[2]:
if strand == "+":
normStart = currStart + max(1,exon[0]-pTup[1])
normEnd = currStart + min(pTup[2]-pTup[1],exon[1]-pTup[1])
else:
normEnd = currStart + min(pTup[2]-pTup[1],pTup[2]-exon[0])
normStart = currStart + max(1,pTup[2] - exon[1])
start_angle, end_angle = start_end_angle(normStart,normEnd,total_length)
patches.append(mpatches.Wedge((0,0), outer_bar-bar_width/2.0, start_angle, end_angle, width=bar_width/2.0))
f_color_v.append('k')
e_color_v.append('k')
lw_v.append(0)
def plot_gene_track(currStart, currEnd, relGenes, pTup, total_length, seg_dir):
overlap_genes.append({})
for gObj in relGenes:
# e_posns is a list of tuples of exon (start,end)
# these can be plotted similarly to how the coding region is marked
gname, gstart, gend, e_posns = gObj.gname, gObj.gstart, gObj.gend, gObj.eposns
seg_len = pTup[2] - pTup[1]
if seg_dir == "+":
normStart = currStart + max(0, gstart - pTup[1])
normEnd = currStart + min(seg_len, gend - pTup[1])
else:
normEnd = currStart + min(seg_len, pTup[2] - gstart)
normStart = currStart + max(0, pTup[2] - gend)
start_angle = normStart / total_length * 360
end_angle = normEnd / total_length * 360
text_angle = (start_angle + end_angle) / 2.0
gene_to_locations[gname].append((start_angle / 360., end_angle / 360.))
if end_angle < 0 and start_angle > 0:
end_angle += 360
patches.append(
mpatches.Wedge((0, 0),
outer_bar,
start_angle,
end_angle,
width=bar_width / 2.0))
f_color_v.append('k')
e_color_v.append('k')
lw_v.append(0)
x_t, y_t = pol2cart(outer_bar + bar_width + 2,
(text_angle / 360 * 2 * np.pi))
# Use filtering from LinearViz to control which names are printed:
'''
if i not in plotted_gene_names or args.print_dup_genes:
print i
'''
text_angle, ha = vu.correct_text_angle(text_angle)
if gname not in overlap_genes[len(overlap_genes) -
2] or gstart > overlap_genes[
len(overlap_genes) - 2].get(gname):
ax.text(x_t,
y_t,
gname,
style='italic',
color='k',
rotation=text_angle,
ha=ha,
va="center",
fontsize=gene_fontsize,
rotation_mode='anchor')
if currEnd < gend:
overlap_genes[len(overlap_genes) - 1][gname] = gend
for exon in e_posns:
if exon[1] > pTup[1] and exon[0] < pTup[2]:
if seg_dir == "+":
normStart = currStart + max(1, exon[0] - pTup[1])
normEnd = currStart + min(pTup[2] - pTup[1],
exon[1] - pTup[1])
else:
normEnd = currStart + min(pTup[2] - pTup[1],
pTup[2] - exon[0])
normStart = currStart + max(1, pTup[2] - exon[1])
start_angle, end_angle = start_end_angle(
normStart, normEnd, total_length)
patches.append(
mpatches.Wedge((0, 0),
outer_bar - bar_width / 2.0,
start_angle,
end_angle,
width=bar_width / 2.0))
f_color_v.append('k')
e_color_v.append('k')
lw_v.append(0)
def plot_ref_genome(ref_placements,
cycle,
total_length,
segSeqD,
imputed_status,
label_segs,
onco_set=set()):
font0 = FontProperties()
p_end = 0
# rot_sp = global_rot / 360. * total_length
for ind, refObj in ref_placements.items():
seg_coord_tup = segSeqD[cycle[ind][0]]
# print(refObj.to_string())
start_angle, end_angle = start_end_angle(refObj.abs_end_pos,
refObj.abs_start_pos,
total_length)
# print start_angle,end_angle
# makes the reference genome wedges
patches.append(
mpatches.Wedge((0, 0),
outer_bar,
end_angle,
start_angle,
width=bar_width))
chrom = segSeqD[cycle[ind][0]][0]
try:
f_color_v.append(chromosome_colors[chrom])
except KeyError:
print("Color not found for " + chrom + ". Using red.")
chromosome_colors[chrom] = "red"
f_color_v.append("red")
e_color_v.append('grey')
lw_v.append(0.2)
# makes the ticks on the reference genome wedges
if cycle[ind][1] == "+":
posns = zip(range(seg_coord_tup[1], seg_coord_tup[2] + 1),
np.arange(refObj.abs_start_pos, refObj.abs_end_pos))
else:
posns = zip(np.arange(seg_coord_tup[2], seg_coord_tup[1] - 1, -1),
np.arange(refObj.abs_start_pos, refObj.abs_end_pos))
tick_freq = max(10000, 30000 * int(np.floor(total_length / 800000)))
#if refObj.abs_end_pos - refObj.abs_start_pos < 30000:
#tick_freq = 25000
# if there are no labels present on the segment given the current frequency, AND this refobject is not adjacent
# to the previous, get positions in this segment divisible by 10kbp, set the middle one as the labelling site
# else just set it to 10000
if (not any(j[0] % tick_freq == 0
for j in posns)) and abs(refObj.abs_start_pos - p_end) > 1:
tens = [j[0] for j in posns if j[0] % 10000 == 0]
middleIndex = (len(tens) - 1) / 2
if tens:
tick_freq = tens[middleIndex]
else:
tick_freq = 10000
p_end = refObj.abs_end_pos
print("tick freq", tick_freq)
for j in posns:
if j[0] % tick_freq == 0:
text_angle = j[1] / total_length * 360
x, y = pol2cart(outer_bar, (text_angle / 360 * 2 * np.pi))
x_t, y_t = pol2cart(outer_bar + 0.2,
(text_angle / 360 * 2 * np.pi))
ax.plot([x, x_t], [y, y_t], color='grey', linewidth=1)
text_angle, ha = vu.correct_text_angle(text_angle)
txt = " " + str(int(round(
(j[0]) / 10000))) if ha == "left" else str(
int(round((j[0]) / 10000))) + " "
ax.text(x_t,
y_t,
txt,
color='grey',
rotation=text_angle,
ha=ha,
va="center",
fontsize=tick_fontsize,
rotation_mode='anchor')
# gene_tree = vu.parse_genes(seg_coord_tup[0], args.ref)
relGenes = vu.rel_genes(gene_tree, seg_coord_tup, copy.copy(onco_set))
# plot the gene track
plot_gene_track(refObj.abs_start_pos, refObj.abs_end_pos, relGenes,
seg_coord_tup, total_length, cycle[ind][1])
# label the segments by number in cycle
mid_sp = (refObj.abs_end_pos + refObj.abs_start_pos) / 2
text_angle = mid_sp / total_length * 360.
x, y = pol2cart((outer_bar - 2 * bar_width),
(text_angle / 360. * 2. * np.pi))
font = font0.copy()
if imputed_status[ind]:
font.set_style('italic')
# font.set_weight('bold')
text_angle, ha = vu.correct_text_angle(text_angle)
if label_segs:
ax.text(x,
y,
cycle[ind][0] + cycle[ind][1],
color='grey',
rotation=text_angle,
ha=ha,
fontsize=5,
fontproperties=font,
rotation_mode='anchor')
def plot_gene_track(currStart, currEnd, relGenes, pTup, total_length, seg_dir, ind, plot_gene_direction=True):
overlap_genes.append({})
for gObj in relGenes:
# e_posns is a list of tuples of exon (start,end)
# these can be plotted similarly to how the coding region is marked
gname, gstart, gend, e_posns = gObj.gname, gObj.gstart, gObj.gend, gObj.eposns
# print(gname, gstart, gend, pTup, len(gObj.gdrops))
seg_len = pTup[2] - pTup[1]
hasStart = False
hasEnd = False
if seg_dir == "+":
ts = max(0, gstart - pTup[1])
te = min(seg_len, gend - pTup[1])
if gObj.strand == "+":
drop = 1.4 * bar_width
if ts > 0: hasStart = True
if te < seg_len: hasEnd = True
else:
drop = 2 * bar_width
if ts > 0: hasEnd = True
if te < seg_len: hasStart = True
normStart = currStart + max(0, gstart - pTup[1])
normEnd = currStart + min(seg_len, gend - pTup[1])
else:
te = min(seg_len, pTup[2] - gstart)
ts = max(0, pTup[2] - gend)
if gObj.strand == "+":
drop = 2 * bar_width
if te < seg_len: hasStart = True
if ts > 0: hasEnd = True
else:
drop = 1.4 * bar_width
if te < seg_len: hasEnd = True
if ts > 0: hasStart = True
normEnd = currStart + min(seg_len, pTup[2] - gstart)
normStart = currStart + max(0, pTup[2] - gend)
start_angle = normStart / total_length * 360
end_angle = normEnd / total_length * 360
text_angle = (start_angle + end_angle) / 2.0
gene_to_locations[gname].append((start_angle / 360., end_angle / 360.))
if end_angle < 0 and start_angle > 0:
end_angle += 360
patches.append(mpatches.Wedge((0, 0), outer_bar, start_angle, end_angle, width=bar_width / 2.0))
f_color_v.append('k')
e_color_v.append('k')
lw_v.append(0)
if gname not in overlap_genes[len(overlap_genes)-2] or gstart > overlap_genes[len(overlap_genes)-2].get(gname)[0]\
or seg_dir != overlap_genes[len(overlap_genes)-2].get(gname)[1]:
x_t, y_t = vu.pol2cart(outer_bar + bar_width + 1.7, (text_angle / 360 * 2 * np.pi))
text_angle, ha = vu.correct_text_angle(text_angle)
if gObj.highlight_name:
ax.text(x_t, y_t, gname, style='italic', color='r', rotation=text_angle, ha=ha, va="center",
fontsize=gene_fontsize, rotation_mode='anchor')
else:
ax.text(x_t, y_t, gname, style='italic', color='k', rotation=text_angle, ha=ha, va="center",
fontsize=gene_fontsize, rotation_mode='anchor')
# draw something to show direction and truncation status
if plot_gene_direction:
plot_gene_direction_indicator(normStart, normEnd, drop)
gObj.gdrops.append((normStart, normEnd, total_length, seg_dir, currStart, currEnd, hasStart, hasEnd, ind, drop, pTup))
# gObj.gdrops = [(normStart, normEnd, total_length, seg_dir, currStart, currEnd, pTup), ]
if currEnd < gend:
overlap_genes[len(overlap_genes)-1][gname] = (gend, seg_dir)
for exon in e_posns:
#fix exon orientation
if exon[1] > pTup[1] and exon[0] < pTup[2]:
if seg_dir == "+":
normStart = currStart + max(1, exon[0] - pTup[1])
normEnd = currStart + min(pTup[2] - pTup[1], exon[1] - pTup[1])
else:
normEnd = currStart + min(pTup[2] - pTup[1], pTup[2] - exon[0])
normStart = currStart + max(1, pTup[2] - exon[1])
start_angle, end_angle = start_end_angle(normStart, normEnd, total_length)
patches.append(
mpatches.Wedge((0, 0), outer_bar - bar_width / 2.0, start_angle, end_angle, width=bar_width / 2.0))
f_color_v.append('k')
e_color_v.append('k')
lw_v.append(0)
