In [1]:

    

%run ~/relmapping/annot/notebooks/__init__.ipynb


    

    




/mnt/home3/jj374/anaconda36/lib/python3.6/site-packages/statsmodels/compat/pandas.py:56: FutureWarning: The pandas.core.datetools module is deprecated and will be removed in a future version. Please use the pandas.tseries module instead.
  from pandas.core import datetools






    




os.getcwd(): /mnt/b2/scratch/ahringer/jj374/lab/relmapping

In [2]:

    

# Load sites and read counts
fp_sites = 'annot/S1_accessible_sites/S1a_accessible_sites.tsv'
df_sites = pd.read_csv(fp_sites, sep='\t')#.query('(atac_source == "atac_wt_pe") | (atac_source == "atac_wt_se")')
df_sites.head()


    

    
Out[2]:







  

    

      

      
chrom
      
start
      
end
      
atac_mode
      
atac_source
      
atac_wt_emb_height
      
atac_wt_l1_height
      
atac_wt_l2_height
      
atac_wt_l3_height
      
atac_wt_l4_height
      
...
      
atac_glp1_d7_rep1_maxcount
      
atac_glp1_d7_rep2_maxcount
      
atac_glp1_d10_rep1_maxcount
      
atac_glp1_d10_rep2_maxcount
      
atac_glp1_d14_rep1_maxcount
      
atac_glp1_d14_rep2_maxcount
      
atac_gon2gem1_ya_rep1_maxcount
      
atac_gon2gem1_ya_rep2_maxcount
      
atac_gon2gem1_d3_rep1_maxcount
      
atac_gon2gem1_d3_rep2_maxcount
    
  
  

    

      
0
      
chrI
      
1870
      
2092
      
1981
      
atac_wt_se
      
1.621415
      
1.459215
      
1.354735
      
1.672520
      
1.204265
      
...
      
33.0
      
33.0
      
36.0
      
42.0
      
28.0
      
58.0
      
28.0
      
32.0
      
33.0
      
59.0
    
    

      
1
      
chrI
      
3809
      
3994
      
3901
      
atac_wt_pe
      
61.688004
      
55.224873
      
69.346062
      
123.587425
      
165.852905
      
...
      
1820.0
      
2072.0
      
1650.0
      
2596.0
      
1316.0
      
1422.0
      
2601.0
      
4677.0
      
2858.0
      
2812.0
    
    

      
2
      
chrI
      
4302
      
4410
      
4356
      
atac_wt_se
      
1.458345
      
2.518715
      
2.017625
      
3.193275
      
5.416205
      
...
      
50.0
      
37.0
      
67.0
      
65.0
      
39.0
      
58.0
      
72.0
      
98.0
      
59.0
      
98.0
    
    

      
3
      
chrI
      
11245
      
11465
      
11355
      
atac_wt_pe
      
2.679690
      
4.330160
      
9.348130
      
10.026175
      
10.876090
      
...
      
452.0
      
554.0
      
412.0
      
668.0
      
314.0
      
555.0
      
371.0
      
458.0
      
375.0
      
416.0
    
    

      
4
      
chrI
      
13087
      
13207
      
13147
      
atac_wt_pe
      
5.160855
      
3.462505
      
3.761785
      
3.173980
      
2.518795
      
...
      
53.0
      
61.0
      
63.0
      
116.0
      
68.0
      
103.0
      
76.0
      
95.0
      
64.0
      
95.0
    
  

5 rows × 72 columns

In [3]:

    

# Peak heights for every hypersensitive site (sizefactor-normalised)
for stage in itertools.islice(config['stages_wt'] + config['stages_glp1'], None):
    print(stage)
    fp_ = pf('atac_%(stage)s' % locals(), 'normalised_coverage', '.bw', 'atac728_geo')
    df_sites['atac_%(stage)s_height_sizefactor' % locals()] = list(map(np.nanmax, yp.read_regions(fp_, df_sites.chrom.tolist(), df_sites.start.tolist(), df_sites.end.tolist())))


    

    




wt_emb
wt_l1
wt_l2
wt_l3
wt_l4
wt_ya
glp1_ya
glp1_d3
glp1_d7
glp1_d10
glp1_d14

In [4]:

    

# Peak heights for every hypersensitive site (SPMR-normalised)
for stage in itertools.islice(config['stages_wt'] + config['stages_glp1'], None):
    print(stage)
    fp_ = pf('atac728_%(stage)s' % locals(), 'tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.macs2_se_extsize150_shiftm75_keepdup_all.mean_by_stage', '.bw', 'atac728')
    df_sites['atac_%(stage)s_height_spmr' % locals()] = list(map(np.nanmax, yp.read_regions(fp_, df_sites.chrom.tolist(), df_sites.start.tolist(), df_sites.end.tolist())))


    

    




wt_emb
wt_l1
wt_l2
wt_l3
wt_l4
wt_ya
glp1_ya
glp1_d3
glp1_d7
glp1_d10
glp1_d14

In [5]:

    

# Peak heights, SPMR-normalised
plt.figure(figsize=(18, 6))
plt.subplot(1, 2, 1)
plt.title('all sites')
df_sites[['atac_%s_height_spmr' % (s,) for s in config['stages_wt'] + config['stages_glp1']]].boxplot()
for tick in plt.gca().get_xticklabels(): tick.set_rotation(90)
plt.gca().set_ylim([0, 20])

df_ = pd.read_csv('annot/S1_accessible_sites/S1a_accessible_sites_with_germline.tsv', sep='\t')
plt.subplot(1, 2, 2)
plt.title('germline')
df_sites.loc[df_['atac_is_germline_specific'], ['atac_%s_height_spmr' % (s,) for s in config['stages_wt'] + config['stages_glp1']]].boxplot()
for tick in plt.gca().get_xticklabels(): tick.set_rotation(90)
plt.gca().set_ylim([0, 20])


    

    
Out[5]:





(0, 20)






    

In [6]:

    

# Peak heights, sizefactor-median normalised
plt.figure(figsize=(18, 6))
plt.subplot(1, 2, 1)
plt.title('all sites')
df_sites[['atac_%s_height_sizefactor' % (s,) for s in config['stages_wt'] + config['stages_glp1']]].boxplot()
for tick in plt.gca().get_xticklabels(): tick.set_rotation(90)
plt.gca().set_ylim([0, 5])

df_ = pd.read_csv('annot/S1_accessible_sites/S1a_accessible_sites_with_germline.tsv', sep='\t')
plt.subplot(1, 2, 2)
plt.title('germline')
df_sites.loc[df_['atac_is_germline_specific'], ['atac_%s_height_sizefactor' % (s,) for s in config['stages_wt'] + config['stages_glp1']]].boxplot()
for tick in plt.gca().get_xticklabels(): tick.set_rotation(90)
plt.gca().set_ylim([0, 5])


    

    
Out[6]:





(0, 5)






    

In [7]:

    

step = 'tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all'
df_spmr = pd.DataFrame()
for rep in itertools.islice(config['stages_wt_by_rep'] + config['stages_glp1_by_rep'], None):
    fp_ = pf('atac728_' + rep, step, '_treat_pileup.bw', 'atac728')
    print(fp_)
    df_spmr[rep] = list(map(np.nanmax, yp.read_regions(fp_, 
        df_sites.chrom.tolist(), df_sites.start.tolist(), df_sites.end.tolist())))


    

    




atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_wt_emb_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_wt_emb_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_wt_l1_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_wt_l1_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_wt_l2_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_wt_l2_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_wt_l3_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_wt_l3_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_wt_l4_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_wt_l4_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_wt_ya_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_wt_ya_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_glp1_ya_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_glp1_ya_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_glp1_d3_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_glp1_d3_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_glp1_d7_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_glp1_d7_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_glp1_d10_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_glp1_d10_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_glp1_d14_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all/atac728_glp1_d14_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_treat_pileup.bw

In [8]:

    

step = 'tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm'
df_sfnorm = pd.DataFrame()
for rep in itertools.islice(config['stages_wt_by_rep'] + config['stages_glp1_by_rep'], None):
    fp_ = pf('atac728_' + rep, step, '.bw', 'atac728')
    print(fp_)
    df_sfnorm[rep] = list(map(np.nanmax, yp.read_regions(fp_, 
        df_sites.chrom.tolist(), df_sites.start.tolist(), df_sites.end.tolist())))


    

    




atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_wt_emb_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_wt_emb_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_wt_l1_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_wt_l1_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_wt_l2_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_wt_l2_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_wt_l3_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_wt_l3_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_wt_l4_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_wt_l4_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_wt_ya_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_wt_ya_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_glp1_ya_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_glp1_ya_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_glp1_d3_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_glp1_d3_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_glp1_d7_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_glp1_d7_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_glp1_d10_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_glp1_d10_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_glp1_d14_rep1.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw
atac728/tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm/atac728_glp1_d14_rep2.tg_se.bwa_se.rm_unmapped.rm_chrM.rm_blacklist.rm_q10.macs2_se_extsize150_shiftm75_keepdup_all_noSPMR.sfnorm.bw

In [13]:

    

# SPMR-normalised
plt.figure(figsize=(18, 12))
plt.subplot(2, 1, 1)
plt.title('all sites')
df_spmr.boxplot()
plt.gca().set_ylim([0, 20])
for tick in plt.gca().get_xticklabels(): tick.set_rotation(45)

plt.subplot(2, 1, 2)
plt.title('germline')
df_ = pd.read_csv('annot/S1_accessible_sites/S1a_accessible_sites_with_germline.tsv', sep='\t')
df_spmr.loc[df_['atac_is_germline_specific']].boxplot()
plt.gca().set_ylim([0, 20])
for tick in plt.gca().get_xticklabels(): tick.set_rotation(45)


    

In [12]:

    

# Sizefactor-normalised
plt.figure(figsize=(18, 12))
plt.title('all sites')
plt.subplot(2, 1, 1)
df_sfnorm.boxplot()
plt.gca().set_ylim([0, 5])
for tick in plt.gca().get_xticklabels(): tick.set_rotation(45)

plt.subplot(2, 1, 2)
plt.title('germline')
df_ = pd.read_csv('annot/S1_accessible_sites/S1a_accessible_sites_with_germline.tsv', sep='\t')
df_sfnorm.loc[df_['atac_is_germline_specific']].boxplot()
plt.gca().set_ylim([0, 5])
for tick in plt.gca().get_xticklabels(): tick.set_rotation(45)


    

In [ ]: