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')
args.ref = "hg38"
if not args.outname:
args.outname = os.path.split(args.cycles_file)[1].split(".")[0]
outdir = os.path.dirname(args.outname)
if outdir and not os.path.exists(outdir):
os.makedirs(outdir)
fname = args.outname + "_path_" + str(args.path) + "_trim_" + str(
args.reduce_path[0]) + "_" + str(args.reduce_path[1])
print(args.reduce_path, "path reduction (L, R)")
print("Reading genes")
gene_tree = vu.parse_genes(args.ref, [])
print("Unaligned fraction cutoff set to " + str(vu.unaligned_cutoff_frac))
chromosome_colors = vu.get_chr_colors()
plt.clf()
fig, ax = plt.subplots(figsize=(10, 6))
patches = []
f_color_v = []
e_color_v = []
lw_v = []
paths, segSeqD, circular_D = vu.parse_cycles_file(args.cycles_file)
path_num = args.path
path = paths[path_num]
if args.ref == "GRCh38":
args.ref = "hg38"
print(args.ref)
if not args.sname:
args.sname = os.path.split(args.cycles_file)[1].split(".")[0] + "_"
outdir = os.path.dirname(args.sname)
if outdir and not os.path.exists(outdir):
os.makedirs(outdir)
fname = args.sname + "cycle_" + args.cycle
print("Reading genes")
gene_tree = vu.parse_genes(args.ref, args.gene_highlight_list)
print("Unaligned fraction cutoff set to " + str(vu.unaligned_cutoff_frac))
chromosome_colors = vu.get_chr_colors()
plt.clf()
fig, ax = plt.subplots()
patches = []
f_color_v = []
e_color_v = []
lw_v = []
cycles, segSeqD, circular_D = vu.parse_cycles_file(args.cycles_file)
cycle_num = args.cycle
isCycle = circular_D[cycle_num]
cycle = cycles[cycle_num]
prev_seg_index_is_adj = vu.adjacent_segs(cycle, segSeqD, isCycle)
def plot_ref_genome(ref_placements,
path,
total_length,
segSeqD,
imputed_status,
label_segs,
onco_set=set()):
font0 = FontProperties()
p_end = 0
for ind, refObj in ref_placements.iteritems():
seg_coord_tup = segSeqD[path[ind][0]]
# print(refObj.to_string())
# start_angle, end_angle = start_end_angle(refObj.abs_end_pos,refObj.abs_start_pos,total_length)
box_len = refObj.abs_end_pos - refObj.abs_start_pos
# print start_angle,end_angle
#makes the reference genome wedges
# patches.append(mpatches.Wedge((0,0), seg_bar_base, end_angle, start_angle, width=bar_width))
patches.append(
mpatches.Rectangle((refObj.abs_start_pos, ref_bar_height), box_len,
bar_width))
chrom = segSeqD[path[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 path[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(40000, 80000 * int(np.floor(total_length / 1000000)))
#segment too small, nothing gets ticked
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
for j in posns:
if j[0] % tick_freq == 0:
x_i, y_i = j[1], ref_bar_height
x_f, y_f = j[1], ref_bar_height - bar_width * 0.3
ax.plot([x_i, x_f], [y_i, y_f], color='grey', linewidth=1)
txt = " " + str(int(round(
(j[0]) / 10000
))) # if ha == "left" else str(int(round((j[0])/10000))) + " "
# txt = str(j[0])
x_t, y_t = j[1], ref_bar_height - bar_width * 0.4
ax.text(x_t,
y_t,
txt,
color='grey',
rotation=-90,
rotation_mode="anchor",
ha="left",
va="center",
fontsize=12)
p_end = refObj.abs_end_pos
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
# TODO: IMPLEMENT
plot_gene_track(refObj.abs_start_pos, relGenes, seg_coord_tup,
total_length, path[ind][1])
#label the segments by number in path
mid_sp = (refObj.abs_end_pos + refObj.abs_start_pos) / 2
# text_angle = mid_sp/total_length*360.
# x,y = pol2cart((seg_bar_base-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')
ax.text(mid_sp,
ref_bar_height + 0.25 * bar_width,
path[ind][0] + path[ind][1],
fontsize=8,
fontproperties=font)
