gwaslab 3.4.38__py3-none-any.whl → 3.4.39__py3-none-any.whl

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Files changed (51) hide show
  1. gwaslab/bd_common_data.py +6 -3
  2. gwaslab/bd_download.py +9 -9
  3. gwaslab/bd_get_hapmap3.py +43 -9
  4. gwaslab/g_Log.py +14 -5
  5. gwaslab/g_Sumstats.py +86 -18
  6. gwaslab/g_SumstatsPair.py +70 -23
  7. gwaslab/g_SumstatsT.py +2 -2
  8. gwaslab/g_version.py +10 -10
  9. gwaslab/hm_casting.py +9 -4
  10. gwaslab/hm_harmonize_sumstats.py +88 -83
  11. gwaslab/io_preformat_input.py +14 -14
  12. gwaslab/io_read_ldsc.py +49 -1
  13. gwaslab/ldsc_irwls.py +198 -0
  14. gwaslab/ldsc_jackknife.py +514 -0
  15. gwaslab/ldsc_ldscore.py +417 -0
  16. gwaslab/ldsc_parse.py +294 -0
  17. gwaslab/ldsc_regressions.py +747 -0
  18. gwaslab/ldsc_sumstats.py +629 -0
  19. gwaslab/qc_check_datatype.py +1 -1
  20. gwaslab/qc_fix_sumstats.py +163 -161
  21. gwaslab/util_ex_calculate_ldmatrix.py +2 -2
  22. gwaslab/util_ex_gwascatalog.py +24 -24
  23. gwaslab/util_ex_ldproxyfinder.py +9 -9
  24. gwaslab/util_ex_ldsc.py +189 -0
  25. gwaslab/util_in_calculate_gc.py +6 -6
  26. gwaslab/util_in_calculate_power.py +42 -43
  27. gwaslab/util_in_convert_h2.py +8 -8
  28. gwaslab/util_in_fill_data.py +28 -28
  29. gwaslab/util_in_filter_value.py +91 -52
  30. gwaslab/util_in_get_density.py +8 -8
  31. gwaslab/util_in_get_sig.py +407 -65
  32. gwaslab/viz_aux_annotate_plot.py +12 -12
  33. gwaslab/viz_aux_quickfix.py +18 -18
  34. gwaslab/viz_aux_reposition_text.py +3 -3
  35. gwaslab/viz_aux_save_figure.py +14 -5
  36. gwaslab/viz_plot_compare_af.py +29 -30
  37. gwaslab/viz_plot_compare_effect.py +63 -71
  38. gwaslab/viz_plot_miamiplot2.py +6 -6
  39. gwaslab/viz_plot_mqqplot.py +17 -3
  40. gwaslab/viz_plot_qqplot.py +1 -1
  41. gwaslab/viz_plot_regionalplot.py +33 -32
  42. gwaslab/viz_plot_rg_heatmap.py +28 -26
  43. gwaslab/viz_plot_stackedregional.py +40 -21
  44. gwaslab/viz_plot_trumpetplot.py +50 -55
  45. gwaslab-3.4.39.dist-info/LICENSE +674 -0
  46. {gwaslab-3.4.38.dist-info → gwaslab-3.4.39.dist-info}/METADATA +4 -3
  47. gwaslab-3.4.39.dist-info/RECORD +80 -0
  48. gwaslab-3.4.38.dist-info/RECORD +0 -72
  49. /gwaslab-3.4.38.dist-info/LICENSE → /gwaslab-3.4.39.dist-info/LICENSE_before_v3.4.39 +0 -0
  50. {gwaslab-3.4.38.dist-info → gwaslab-3.4.39.dist-info}/WHEEL +0 -0
  51. {gwaslab-3.4.38.dist-info → gwaslab-3.4.39.dist-info}/top_level.txt +0 -0
gwaslab/viz_plot_trumpetplot.py CHANGED
@@ -108,36 +108,34 @@ def plottrumpet(mysumstats,
108
108
  scatter_args["color"]=markercolor
109
109
 
110
110
  #Checking columns#################################################################################################################
111
- if verbose: log.write("Start to create trumpet plot...")
111
+ log.write("Start to create trumpet plot...", verbose=verbose)
112
112
 
113
113
  #parameter check##################################################################################################################
114
114
  if (beta not in mysumstats.columns) or (eaf not in mysumstats.columns):
115
- if verbose:
116
- log.write(" -No EAF or BETA columns. Skipping...")
115
+ log.write(" -No EAF or BETA columns. Skipping...", verbose=verbose)
117
116
  return None
118
117
  if mode=="b":
119
118
  if ncase is None or ncontrol is None:
120
- if verbose:
121
- log.write(" -No scase or scontrol. Skipping...")
119
+ log.write(" -No scase or scontrol. Skipping...", verbose=verbose)
122
120
  return None
123
121
  if prevalence is None:
124
122
  prevalence= ncase/(ncase + ncontrol)
125
- log.write(" -Prevalence is not given. Estimating based on scase and scontrol :{}...".format(prevalence))
123
+ log.write(" -Prevalence is not given. Estimating based on scase and scontrol :{}...".format(prevalence), verbose=verbose)
126
124
 
127
125
  #print settings##################################################################################################################
128
- if verbose:
129
- log.write(" -Settings:")
130
- log.write(" -Mode: {}".format(mode))
131
- if mode == "q" :
132
- log.write(" -N: {}".format(n))
133
- if mode == "b" :
134
- log.write(" -N_CASE: {}".format(ncase))
135
- log.write(" -N_CONTROL: {}".format(ncontrol))
136
- log.write(" -PREVALENCE: {}".format(prevalence))
137
- log.write(" -BETA: {}".format(beta))
138
- log.write(" -Significance level: {}".format(sig_level))
139
- log.write(" -Power thresholds: {}".format(ts))
140
- log.write(" -Power line smoothness: {}".format(n_matrix))
126
+
127
+ log.write(" -Settings:", verbose=verbose)
128
+ log.write(" -Mode: {}".format(mode), verbose=verbose)
129
+ if mode == "q" :
130
+ log.write(" -N: {}".format(n), verbose=verbose)
131
+ if mode == "b" :
132
+ log.write(" -N_CASE: {}".format(ncase), verbose=verbose)
133
+ log.write(" -N_CONTROL: {}".format(ncontrol), verbose=verbose)
134
+ log.write(" -PREVALENCE: {}".format(prevalence), verbose=verbose)
135
+ log.write(" -BETA: {}".format(beta), verbose=verbose)
136
+ log.write(" -Significance level: {}".format(sig_level), verbose=verbose)
137
+ log.write(" -Power thresholds: {}".format(ts), verbose=verbose)
138
+ log.write(" -Power line smoothness: {}".format(n_matrix), verbose=verbose)
141
139
 
142
140
  #loading columns #################################################################################################################
143
141
  cols_to_use = [snpid, beta, eaf, n, p]
@@ -145,7 +143,7 @@ def plottrumpet(mysumstats,
145
143
  if anno is not None:
146
144
  if anno != "GENENAME":
147
145
  if anno!=True:
148
- log.write(" -Loading column {} for annotation...".format(anno))
146
+ log.write(" -Loading column {} for annotation...".format(anno), verbose=verbose)
149
147
  if anno not in cols_to_use:
150
148
  cols_to_use.append(anno)
151
149
  else:
@@ -160,17 +158,17 @@ def plottrumpet(mysumstats,
160
158
  #filter by p #################################################################################################################
161
159
  if p in mysumstats.columns:
162
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  sumstats = mysumstats.loc[mysumstats[p]< p_level,cols_to_use ].copy()
163
- if verbose: log.write(" -Excluding variants with P values > {}".format(p_level))
161
+ log.write(" -Excluding variants with P values > {}".format(p_level), verbose=verbose)
164
162
  else:
165
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  cols_to_use.remove(p)
166
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  sumstats = mysumstats[[beta,eaf,n]].copy()
167
- if verbose: log.write(" -Plotting {} variants...".format(len(sumstats)))
165
+ log.write(" -Plotting {} variants...".format(len(sumstats)), verbose=verbose)
168
166
 
169
167
  #add maf column #################################################################################################################
170
168
  if maf not in sumstats.columns:
171
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  sumstats = filldata(sumstats,to_fill=["MAF"],verbose=False)
172
170
  is_filpped = (sumstats["MAF"] < sumstats[eaf]) & (sumstats[eaf] > 0.5)& (sumstats["MAF"] < 0.5)
173
- if verbose: log.write(" -Flipping {} variants...".format(sum(is_filpped)))
171
+ log.write(" -Flipping {} variants...".format(sum(is_filpped)), verbose=verbose)
174
172
  sumstats.loc[is_filpped, beta] = -sumstats.loc[is_filpped, beta]
175
173
 
176
174
  #configure n #################################################################################################################
@@ -185,8 +183,7 @@ def plottrumpet(mysumstats,
185
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  n = sumstats["N"].median()
186
184
  elif n == "mean":
187
185
  n = sumstats["N"].mean()
188
- if verbose:
189
- log.write(" -N for power calculation: {}".format(n))
186
+ log.write(" -N for power calculation: {}".format(n), verbose=verbose)
190
187
 
191
188
  #configure beta and maf range ###################################################################################################
192
189
  if maf_range is None:
@@ -419,7 +416,7 @@ def plottrumpet(mysumstats,
419
416
  elif mode=="b":
420
417
  save_figure(fig, save, keyword="trumpet_b",save_args=save_args, log=log, verbose=verbose)
421
418
 
422
- if verbose: log.write("Finished creating trumpet plot!")
419
+ log.write("Finished creating trumpet plot!", verbose=verbose)
423
420
  return fig
424
421
 
425
422
  ####################################################################
@@ -469,12 +466,11 @@ def plot_power( ns=1000,
469
466
  xticklabels = xticks
470
467
 
471
468
  #Checking columns#################################################################################################################
472
- if verbose: log.write("Start to create trumpet plot...")
469
+ log.write("Start to create trumpet plot...", verbose=verbose)
473
470
 
474
471
  if mode=="b":
475
472
  if ncases is None or ncontrols is None:
476
- if verbose:
477
- log.write(" -No scase or scontrol. Skipping...")
473
+ log.write(" -No scase or scontrol. Skipping...", verbose=verbose)
478
474
  return None
479
475
 
480
476
  #configure beta and maf range ###################################################################################################
@@ -628,7 +624,7 @@ def plot_power( ns=1000,
628
624
  elif mode=="b":
629
625
  save_figure(fig, save, keyword="power_b",save_args=save_args, log=log, verbose=verbose)
630
626
 
631
- if verbose: log.write("Finished creating trumpet plot!")
627
+ log.write("Finished creating trumpet plot!", verbose=verbose)
632
628
  return fig
633
629
 
634
630
 
@@ -667,29 +663,29 @@ def plot_power_x(
667
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  log=Log()):
668
664
 
669
665
  #Checking columns#################################################################################################################
670
- if verbose: log.write("Start to create power plot...")
666
+ log.write("Start to create power plot...", verbose=verbose)
671
667
  matplotlib.rc('font', family=font_family)
672
- if verbose:
673
- log.write(" -Settings:")
674
- log.write(" -Mode: {}".format(mode))
675
- if mode == "q" :
676
- log.write(" -X axis: {}".format(x))
677
- if x!="N":
678
- log.write(" -N: {}".format(ns))
679
- if x!="MAF":
680
- log.write(" -MAF: {}".format(mafs))
681
- if mode == "b" :
682
- log.write(" -X axis: {}".format(x))
683
- if x!="N_CASE":
684
- log.write(" -N_CASE: {}".format(ncases))
685
- if x!="N_CASE":
686
- log.write(" -N_CONTROL: {}".format(ncontrols))
687
- if x!="PREVALENCE":
688
- log.write(" -PREVALENCE: {}".format(prevalences))
689
- if x!="BETA":
690
- log.write(" -BETA: {}".format(betas))
691
-
692
- log.write(" -Significance level: {}".format(sig_levels))
668
+
669
+ log.write(" -Settings:", verbose=verbose)
670
+ log.write(" -Mode: {}".format(mode), verbose=verbose)
671
+ if mode == "q" :
672
+ log.write(" -X axis: {}".format(x), verbose=verbose)
673
+ if x!="N":
674
+ log.write(" -N: {}".format(ns), verbose=verbose)
675
+ if x!="MAF":
676
+ log.write(" -MAF: {}".format(mafs), verbose=verbose)
677
+ if mode == "b" :
678
+ log.write(" -X axis: {}".format(x), verbose=verbose)
679
+ if x!="N_CASE":
680
+ log.write(" -N_CASE: {}".format(ncases), verbose=verbose)
681
+ if x!="N_CASE":
682
+ log.write(" -N_CONTROL: {}".format(ncontrols), verbose=verbose)
683
+ if x!="PREVALENCE":
684
+ log.write(" -PREVALENCE: {}".format(prevalences), verbose=verbose)
685
+ if x!="BETA":
686
+ log.write(" -BETA: {}".format(betas), verbose=verbose)
687
+
688
+ log.write(" -Significance level: {}".format(sig_levels), verbose=verbose)
693
689
 
694
690
  if x is None:
695
691
  if mode=="b":
@@ -707,8 +703,7 @@ def plot_power_x(
707
703
 
708
704
  if mode=="b":
709
705
  if ncases is None or ncontrols is None:
710
- if verbose:
711
- log.write(" -No scase or scontrol. Skipping...")
706
+ log.write(" -No scase or scontrol. Skipping...", verbose=verbose)
712
707
  return None
713
708
 
714
709
  #configure beta and maf range ###################################################################################################
@@ -923,5 +918,5 @@ def plot_power_x(
923
918
  elif mode=="b":
924
919
  save_figure(fig, save, keyword="power_xb",save_args=save_args, log=log, verbose=verbose)
925
920
 
926
- if verbose: log.write("Finished creating power plot!")
921
+ log.write("Finished creating power plot!", verbose=verbose)
927
922
  return fig