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_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_bpg_connection(ref_placements, prev_seg_index_is_adj, bpg_dict,
seg_end_pos_d):
connect_width = bar_width / 2.
for ind, refObj in ref_placements.items():
next_ind = (ind + 1) % len(ref_placements)
next_refObj = ref_placements[next_ind]
if not prev_seg_index_is_adj[
next_ind]: # or next_ind == 0 to try and close
bpg_adjacency = vu.pair_is_edge(refObj.id, next_refObj.id,
refObj.direction,
next_refObj.direction, bpg_dict,
seg_end_pos_d)
if not bpg_adjacency or ind == len(ref_placements) - 1:
continue
bpg_connector_len = next_refObj.abs_start_pos - refObj.abs_end_pos
# makes the reference genome wedges
patches.append(
mpatches.Rectangle(
(refObj.abs_end_pos, ref_bar_height + bar_width / 4.),
bpg_connector_len, connect_width))
f_color_v.append('grey')
e_color_v.append('grey')
lw_v.append(0.2)
def construct_path_ref_placements(path,
segSeqD,
raw_path_length,
prev_seg_index_is_adj,
next_seg_index_is_adj,
cycle_seg_counts,
aln_vect=None):
if aln_vect is None:
aln_vect = []
spacing_bp = seg_spacing * raw_path_length
path_ref_placements = {}
curr_start = 0.0
for ind, i in enumerate(path):
seg_id_count = cycle_seg_counts[i[0]]
seg_len = segSeqD[i[0]][2] - segSeqD[i[0]][1]
seg_end = curr_start + seg_len
padj, nadj = prev_seg_index_is_adj[ind], next_seg_index_is_adj[ind]
curr_obj = vu.CycleVizElemObj(i[0], segSeqD[i[0]][0], segSeqD[i[0]][1],
segSeqD[i[0]][2], i[1], curr_start,
seg_end, seg_id_count, padj, nadj)
path_ref_placements[ind] = curr_obj
next_start = seg_end
mod_ind = (ind + 1) % (len(prev_seg_index_is_adj))
if not prev_seg_index_is_adj[mod_ind]:
next_start += spacing_bp
curr_start = next_start
total_length = next_start
return path_ref_placements, total_length
def plot_bpg_connection(ref_placements, cycle, total_length,
prev_seg_index_is_adj, bpg_dict, seg_end_pos_d):
connect_width = bar_width / 2.
for ind, refObj in ref_placements.items():
next_ind = (ind + 1) % len(ref_placements)
next_refObj = ref_placements[next_ind]
if not prev_seg_index_is_adj[
next_ind]: # or next_ind == 0 to try and close
bpg_adjacency = vu.pair_is_edge(refObj.id, next_refObj.id,
refObj.direction,
next_refObj.direction, bpg_dict,
seg_end_pos_d)
if not bpg_adjacency:
continue
start_angle, end_angle = start_end_angle(next_refObj.abs_start_pos,
refObj.abs_end_pos,
total_length)
# makes the reference genome wedges
patches.append(
mpatches.Wedge((0, 0),
outer_bar - bar_width / 4,
end_angle,
start_angle,
width=connect_width))
f_color_v.append('grey')
e_color_v.append('grey')
lw_v.append(0.2)
def plot_alignment(contig_locs, segment_locs, total_length):
segs_base = outer_bar + segment_bar_height
linewidth = min(0.25 * 2000000 / total_length, 0.25)
for a_d in aln_vect:
c_id = a_d["contig_id"]
c_num_dir = int(a_d["contig_dir"] + "1")
contig_label_vect = contig_locs[c_id].label_posns
seg_label_vect = segment_locs[a_d["seg_aln_number"]].label_posns
c_l_pos = contig_label_vect[a_d["contig_label"] - 1]
c_l_loc = c_l_pos / total_length * 2. * np.pi
# s_l_pos = seg_label_vect[s_num_dir*a_d["seg_label"]-(s_num_dir+1)/2]
s_l_pos = seg_label_vect[a_d["seg_label"] - 1]
s_l_loc = s_l_pos / total_length * 2. * np.pi
contig_top = outer_bar + contig_bar_height + contig_locs[c_id].track_height_shift + bar_width
x_c, y_c = vu.pol2cart(contig_top, c_l_loc)
x_s, y_s = vu.pol2cart(segs_base, s_l_loc)
ax.plot([x_c, x_s], [y_c, y_s], color="grey", linewidth=linewidth)
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 construct_cycle_ref_placements(cycle,segSeqD,raw_cycle_length,prev_seg_index_is_adj,isCycle,aln_vect = []):
spacing_bp = seg_spacing*raw_cycle_length
cycle_ref_placements = {}
curr_start = 0.0 if isCycle else spacing_bp
for ind,i in enumerate(cycle):
seg_len = segSeqD[i[0]][2] - segSeqD[i[0]][1]
seg_end = curr_start+seg_len
curr_obj = vu.CycleVizElemObj(i[0],i[1],curr_start,seg_end)
cycle_ref_placements[ind] = curr_obj
next_start = seg_end
mod_ind = (ind+1) % (len(prev_seg_index_is_adj))
if not prev_seg_index_is_adj[mod_ind]:
next_start+=spacing_bp
curr_start = next_start
total_length = next_start
return cycle_ref_placements,total_length
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')
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]
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)
parser.add_argument("--sname", help="output prefix")
parser.add_argument("--rot", help="number of segments to rotate counterclockwise", type=int, default=0)
parser.add_argument("--label_segs", help="label segs with graph IDs", action='store_true')
parser.add_argument("--gene_subset_file", help="file containing subset of genes to plot (e.g. oncogene genelist file)",
default="")
parser.add_argument("--gene_subset_list", help="list of genes to plot (e.g. MYC PVT1)", nargs="+", type=str)
parser.add_argument("--print_dup_genes", help="if a gene appears multiple times print name every time.",
action='store_true', default=False)
parser.add_argument("--gene_highlight_list", help="list of gene names to highlight", nargs="+", type=str, default=[])
parser.add_argument("--gene_fontsize", help="font size for gene names", type=float, default=7)
parser.add_argument("--tick_fontsize", help="font size for genomic position ticks", type=float, default=7)
parser.add_argument("--bedgraph", help="bedgraph file specifying additional data")
args = parser.parse_args()
if args.yaml_file:
args = vu.parse_yaml(args)
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")