def yield_pathway_names(self, karyotype):
for chromosome in self.chromosomes:
name= Abbrator(chromosome.name, 15, upper= False, pathway=True).abbr
name= name.capitalize()
self.abbreviations[chromosome.name] = name
coors= chromosome.get_coordinates()
first= coors[0].get_coordinate()[1]
karyotype_name= coors[0].get_name_by_level(1)
last= coors[-1].get_coordinate()[1]
coor= (first + last)/2
line= map(str, [karyotype[karyotype_name], coor, coor, name])
yield "\t".join(line)+"\n"
def yield_text(self, karyotype, coors_between_letters=100):
"""
self.karyotype
Abbrator
"""
### below parameters are related to the karyotype size!!1
### TODO adjust them accordingly!!!!
### factors: directionality, color
###
#" current problems:
# 1 highlights and text coordinates do not match with the heatmap coordinates. check it out
# 2 spaces between words should not take 3 times the siz of an empty character.
# 3 ....
coor_step_size= 5
total_coordinate_len= len(self.get_all_coordinates())
total_ideogram_len= total_coordinate_len * coor_step_size
### broadest level will fit more letters.
if self.level == 1:
total_letters= 190
elif self.level == 2:
total_letters= 180
### total number of letters that an ideogram (circle) can fit
#total_letters= 180
### length of a character in coordinate units
char_len= total_ideogram_len / total_letters
if self.calculation_type == "sum":
values= sorted([chrom.get_unique_total_value() for chrom in self.chromosomes])
#global_total_value= self.get_total_value()
elif self.calculation_type == "average":
values= sorted([chrom.get_unique_average_value() for chrom in self.chromosomes])
#global_total_value = self.get_average_value()
heat_stop_1= int(0.8* len(self.chromosomes))
heat_stop_2= int(0.5* len(self.chromosomes))
threshold1= values[heat_stop_1]
threshold2= values[heat_stop_2]
### avg does not work in our case. check what are the light
### colors and what are the dark colors in the circos coloring
### scheme. in worst case, color dark if the abundance level s
### lower than 2/3 instead of averadge.
for chrom in self.chromosomes:
name= chrom.name
coordinate_len= len(chrom.get_coordinates())
chromosome_len= coordinate_len * coor_step_size
allowed_char_n = int(chromosome_len / char_len)
abbr_pathway= Abbrator(name, allowed_char_n).abbr
karyotype_name= chrom.get_coordinates()[0].get_name_by_level(1).strip()
### there is enough space after the abbreviation for sure
self.abbreviations[name] = abbr_pathway
### center the label in the ideogram
### update the pathway abbreviation according to blank penalty rules
abbr_pathway= abbr_pathway.replace('.', '')
free_space= chromosome_len - (len(abbr_pathway) * char_len)
free_coors= free_space / coor_step_size
init_coor= free_coors / 2
if init_coor < 0 : init_coor= 0
options= ""
if self.calculation_type == "sum":
total= chrom.get_unique_total_value()
elif self.calculation_type == "average":
total= chrom.get_unique_average_value()
if total < threshold2:
color = "vdgrey"
elif total >= threshold2 and total < threshold1:
color= "vvdgrey"
else:
color = "white"
option1= "color=%s" %color
## below options did not work
#option2= "label_snuggle=yes"
#option3= "label_parallel=no"
#options= ",".join([option1, option2, option3])
options= option1
blank_penalty= 0
for i in range(len(abbr_pathway)):
#coor_index= int(init_coor) + int(i * char_len / coor_step_size)
coor_index= int(init_coor) + (int(init_coor) + int(i * char_len)) / coor_step_size
#if self.level == 2:
# pdb.set_trace()
coor= chrom.get_coordinates()[coor_index]
letter= abbr_pathway[i]
if letter == " ":
blank_penalty+=1
#line = [karyotype[karyotype_name], str(startCoor),
# str(startCoor + int(char_len)), letter, options]
#yield "\t".join(line)+'\n'
else:
#if letter == ".":
# blank_penalty += 1
# continue
penalty= blank_penalty * int(char_len) / 3
crs= coor.get_coordinate()
### we have to also update the init_coor accordingly
startCoor= crs[0] - int(penalty)
line = [karyotype[karyotype_name], str(startCoor),
str(startCoor + int(char_len)), letter, options]
yield "\t".join(line)+'\n'
