plotting

Functions to plot mutation results

read_ref_file="sacB_ref.fasta"
ref=next(SeqIO.parse(os.path.join(data_path,read_ref_file),"fasta"))


#read_ref_file="\\sacB_ref.fasta"
#ref=next(SeqIO.parse(data_path+read_ref_file,'fasta'))

ref_seq=str(ref.seq)
gen_list=parse_genotypes(os.path.join(data_path,"sacB_genotypes.csv"))

# read_ref_file_paul='/home/prochett/DGRec/dgrec/example_data/sacB_ref.fasta'
# ref_paul=next(SeqIO.parse(os.path.join(data_path,read_ref_file_paul),"fasta"))

# ref_seq=str(ref_paul.seq)
# gen_list=[]
# with open(os.path.join(data_path,"/home/prochett/DGRec/dgrec/example_data/sacB_genotypes.csv"),"r") as handle: 
#     reader = csv.reader(handle, delimiter='\t')
#     for row in reader:
#         gen_list.append((row[0],int(row[1])))

---

source

plot_mutations

 plot_mutations (gen_list:list, ref_seq:str, sample_name:str=None,
                 plot_range:Union[tuple,list]=None,
                 TR_range:Union[tuple,list]=None, ax=None)

	Type	Default	Details
gen_list	list		list of genotypes. Each genotype is a tuple: (string representation of the genotype, number of molecules)
ref_seq	str		reference sequence
sample_name	str	None	sample name
plot_range	Union	None	limits the plot to the specified range
TR_range	Union	None	when specified creates a shaded box highlighting the position of the TR
ax	NoneType	None	makes it possible to pass matplotlib axis to easily configure and save plots

---

source

plot_mutations_percentage

 plot_mutations_percentage (gen_list:list, ref_seq:str,
                            sample_name:str=None,
                            plot_range:Union[tuple,list]=None,
                            TR_range:Union[tuple,list]=None,
                            rev_comp=False, ax=None)

	Type	Default	Details
gen_list	list		list of genotypes. Each genotype is a tuple: (string representation of the genotype, number of molecules)
ref_seq	str		reference sequence
sample_name	str	None	sample name
plot_range	Union	None	limits the plot to the specified range
TR_range	Union	None	when specified creates a shaded box highlighting the position of the TR
rev_comp	bool	False
ax	NoneType	None	makes it possible to pass matplotlib axis to easily configure and save plots

ax = plot_mutations(gen_list, ref_seq, sample_name="sacB", plot_range=[0,139], TR_range=[50,119])

ax,mut_perc=plot_mutations_percentage(gen_list, ref_seq, sample_name="sacB", plot_range=[0,139], TR_range=[50,119])
plt.show
print(mut_perc)

9.73

ax = plot_mutations_percentage(gen_list, ref_seq, sample_name="sacB", plot_range=[0,139], TR_range=[20,89],rev_comp=True)

---

source

plot_mutations_percentage_protein

 plot_mutations_percentage_protein (aa_mut_list, ref_prot,
                                    plot_range=None, ax=None)

	Type	Default	Details
aa_mut_list			list of genotypes. Each genotype is a tuple: (string representation of the genotype, number of molecules)
ref_prot			reference sequence
plot_range	NoneType	None	limits the plot to the specified range
ax	NoneType	None

aa_mut_list=get_aa_mut_list(gen_list,ref_seq,ori=-1) #the sacB gene is in reverse complement orientation compared to the VR so ori=-1 is needed
aa_mut_list[:10]

[('', 43341),
 ('Y22H', 351),
 ('H15Q', 277),
 ('D19E', 246),
 ('L17P', 200),
 ('V23A', 162),
 ('S11P', 117),
 ('D25E', 113),
 ('D19E,Y22H', 75),
 ('T16P', 61)]

ref_prot=Seq(ref_seq).reverse_complement()[:-1].translate() #the sacB gene is in reverse complement orientation compared to the VR

fig, ax = plt.subplots(1, 1, figsize=(20, 5))
plot_mutations_percentage_protein(aa_mut_list, ref_prot, ax=ax)
plt.show()

/tmp/ipykernel_1816/3434536392.py:11: MatplotlibDeprecationWarning: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead.
  colormap = cm.get_cmap(colormap_name, num_colors)