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_ref_genome(ref_placements,
path,
total_length,
segSeqD,
imputed_status,
label_segs,
color_map,
onco_set=None):
if onco_set is None:
onco_set = set()
font0 = FontProperties()
p_end = 0
for ind, refObj in ref_placements.items():
print(ind, refObj.to_string(), ref_bar_height)
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_height, 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]
if color_map == "standard":
try:
c_col = chromosome_colors[chrom]
except KeyError:
print("Color not found for " + chrom + ". Using red.")
chromosome_colors[chrom] = "red"
c_col = chromosome_colors[chrom]
else:
c_col = color_map(float(refObj.id) / len(segSeqD))
f_color_v.append(c_col)
e_color_v.append(c_col)
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 # do integer division
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
plot_gene_track(refObj.abs_start_pos, refObj.abs_end_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_height-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')
label_text = path[ind][1]
if label_segs == "id":
label_text = path[ind][0] + label_text
ax.text(mid_sp,
ref_bar_height + 0.25 * bar_width,
label_text,
fontsize=8,
fontproperties=font,
ha='center')
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')