gwaslab 3.5.0__py3-none-any.whl → 3.5.1__py3-none-any.whl

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Files changed (18) hide show
  1. gwaslab/bd_get_hapmap3.py +3 -1
  2. gwaslab/g_Sumstats.py +8 -8
  3. gwaslab/g_version.py +2 -2
  4. gwaslab/io_process_args.py +23 -0
  5. gwaslab/qc_fix_sumstats.py +9 -5
  6. gwaslab/vis_plot_credible sets.py +0 -0
  7. gwaslab/viz_aux_annotate_plot.py +8 -0
  8. gwaslab/viz_aux_property.py +2 -0
  9. gwaslab/viz_plot_compare_effect.py +787 -468
  10. gwaslab/viz_plot_mqqplot.py +4 -1
  11. gwaslab/viz_plot_phe_heatmap.py +1 -1
  12. gwaslab/viz_plot_stackedregional.py +1 -1
  13. {gwaslab-3.5.0.dist-info → gwaslab-3.5.1.dist-info}/METADATA +3 -3
  14. {gwaslab-3.5.0.dist-info → gwaslab-3.5.1.dist-info}/RECORD +18 -15
  15. {gwaslab-3.5.0.dist-info → gwaslab-3.5.1.dist-info}/WHEEL +1 -1
  16. {gwaslab-3.5.0.dist-info → gwaslab-3.5.1.dist-info}/LICENSE +0 -0
  17. {gwaslab-3.5.0.dist-info → gwaslab-3.5.1.dist-info}/LICENSE_before_v3.4.39 +0 -0
  18. {gwaslab-3.5.0.dist-info → gwaslab-3.5.1.dist-info}/top_level.txt +0 -0
gwaslab/viz_plot_mqqplot.py CHANGED
@@ -139,6 +139,7 @@ def mqqplot(insumstats,
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  anno_gtf_path=None,
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  anno_adjust=False,
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  anno_max_iter=100,
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+ arrow_kwargs=None,
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  arm_offset=None,
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  arm_scale=1,
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  anno_height=1,
@@ -243,7 +244,8 @@ def mqqplot(insumstats,
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  anno_args=dict()
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  if colors is None:
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  colors=["#597FBD","#74BAD3"]
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-
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+ if arrow_kwargs is None:
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+ arrow_kwargs=dict()
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  if region is not None:
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  if marker_size == (5,20):
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  marker_size=(45,65)
@@ -1002,6 +1004,7 @@ def mqqplot(insumstats,
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  region_anno_bbox_args=region_anno_bbox_args,
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  skip=skip,
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  anno_height=anno_height,
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+ arrow_kwargs=arrow_kwargs,
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  snpid=snpid,
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  chrom=chrom,
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  pos=pos,
gwaslab/viz_plot_phe_heatmap.py CHANGED
@@ -203,7 +203,7 @@ def _gwheatmap(
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  linewidth=linewidth,
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  edgecolor = edgecolor,
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  zorder=2,
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- ax=ax1)
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+ ax=ax1, **scatter_kwargs)
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  handles, labels = ax1.get_legend_handles_labels()
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  new_labels = []
gwaslab/viz_plot_stackedregional.py CHANGED
@@ -143,7 +143,7 @@ def plot_stacked_mqq(objects,
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  mqq_args_for_each_plot = _sort_args(mqq_args, n_plot)
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  ##########################################################################################################################################
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  # get x axis dict
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- if mode=="m":
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+ if mode=="m" or mode=="r":
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  _posdiccul = _get_chrom_dic(sumstats_list,chrom="CHR",pos="POS",chrpad=0.02)
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  else:
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  _posdiccul=None
{gwaslab-3.5.0.dist-info → gwaslab-3.5.1.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: gwaslab
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- Version: 3.5.0
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+ Version: 3.5.1
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  Summary: A collection of handy tools for GWAS SumStats
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  Author-email: Yunye <yunye@gwaslab.com>
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  Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -20,7 +20,7 @@ Requires-Dist: scipy>=1.12
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  Requires-Dist: pySAM==0.22.1
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  Requires-Dist: Biopython>=1.79
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  Requires-Dist: adjustText<=0.8,>=0.7.3
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- Requires-Dist: liftover>=1.1.13
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+ Requires-Dist: liftover<=1.3.1,>=1.1.13
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  Requires-Dist: scikit-allel>=1.3.5
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  Requires-Dist: pyensembl==2.2.3
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  Requires-Dist: gtfparse==1.3.0
@@ -51,7 +51,7 @@ Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/
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  ### install via pip
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  ```
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- pip install gwaslab==3.4.46
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+ pip install gwaslab==3.5.0
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  ```
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  ```python
{gwaslab-3.5.0.dist-info → gwaslab-3.5.1.dist-info}/RECORD RENAMED
@@ -2,21 +2,22 @@ gwaslab/__init__.py,sha256=7TKJaODdpeuQKibL7gIEa4MtyQ0pmrU-vIHQ-Et27lQ,2433
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  gwaslab/bd_common_data.py,sha256=2voBqMrIsII1TN5T6uvyDax90fWcJK1Stmo1ZHNGGsE,13898
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  gwaslab/bd_config.py,sha256=TP-r-DPhJD3XnRYZbw9bQHXaDIkiRgK8bG9HCt-UaLc,580
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  gwaslab/bd_download.py,sha256=cDDk2C5IvjeAzvPvVYGTkI4Ss33DUtEDjGo8eAbQRvY,15663
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- gwaslab/bd_get_hapmap3.py,sha256=asNjQYeGfQi8u3jnfenRvDdKMs5ptql5wpcUzqMlwUI,3937
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+ gwaslab/bd_get_hapmap3.py,sha256=FQpwbhWUPFT152QtiLevEkkN4YcVDIeKzoK0Uz1NlRo,4108
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  gwaslab/cache_manager.py,sha256=HOTnSkCOyGEPLRl90WT8D_6pAdI8d8AzenMIDGuCeWc,28113
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  gwaslab/g_Log.py,sha256=C3Zv-_6c3C9ms8bgQ-ytplz22sjk7euqXYkWr9zNeAs,1573
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  gwaslab/g_Phenotypes.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- gwaslab/g_Sumstats.py,sha256=6bzc7Sf23fIZRP85h-hQJC8DsBl3YLZNBUKJaOboHJQ,36639
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+ gwaslab/g_Sumstats.py,sha256=c_qYY2H-nf-JtGepzafoHuYwnWxmOOBf9CDytPZc60Q,36704
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  gwaslab/g_SumstatsPair.py,sha256=20snPb4SlI6ftMGVjgxAuyxsxYRQF-GzzlBSnoB-3Lo,8851
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  gwaslab/g_SumstatsT.py,sha256=u_DighLMnMxwTLnqm-B58pA0G6WXRj6pudPyKMVKjSU,2133
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  gwaslab/g_Sumstats_summary.py,sha256=FECvvFXJVKaCX5dggBvvk9YvJ6AbdbcLfjltysX7wEE,6380
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  gwaslab/g_meta.py,sha256=htWlgURWclm9R6UqFcX1a93WN27xny7lGUeyJZOtszQ,2583
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  gwaslab/g_vchange_status.py,sha256=w3zsYYOcCaI3PTeboonvkQjudzUAfVIgATzRdiPViZs,1939
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- gwaslab/g_version.py,sha256=ll9kIVGycz_99ofwzsFd_semBDePvcEjIqqCgWdVa_8,1885
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+ gwaslab/g_version.py,sha256=Wpfo8Y_fjYS4ajalombaHrLezBO7BOr070GnjQHhOGw,1885
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  gwaslab/hm_casting.py,sha256=FqP4EQl83Q2OKLw004OgLIvUH795TVCGwziLk5jsHqY,11368
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  gwaslab/hm_harmonize_sumstats.py,sha256=_sZ8soikAxDokw-dcr_CLguBB8OmTmPPS04MfmsJc_Q,79509
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  gwaslab/hm_rsid_to_chrpos.py,sha256=ODWREO0jPN0RAfNzL5fRzSRANfhiksOvUVPuEsFZQqA,6552
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  gwaslab/io_preformat_input.py,sha256=J8Ny4OPMaLVdo2nP8lTM-c5A8LSdqphSrp9G4i9JjDQ,24097
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+ gwaslab/io_process_args.py,sha256=bF7oHBtMnxJgksIit0O0_U94dZFh8r5YblgDqEEsqoM,806
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  gwaslab/io_read_ldsc.py,sha256=wsYXpH50IchBKd2dhYloSqc4YgnDkiwMsAweaCoN5Eo,12471
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  gwaslab/io_read_tabular.py,sha256=EG-C6KhCutt4J4LlOMgXnqzJvU-EZXzVhMvaDFnHrMM,2380
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  gwaslab/io_to_formats.py,sha256=8FmbQjWUIsz_V1Lb80TuwRIXKBgs5t42j25Znougk1Y,29401
@@ -28,7 +29,7 @@ gwaslab/ldsc_parse.py,sha256=MBnfgcWlV4oHp9MoDRh1mpilaHhAR15Af77hMFn4-5k,10564
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  gwaslab/ldsc_regressions.py,sha256=yzbGjgNV7u-SWXNPsh9S8y9mK97Bim_Nmad9G9V18ZU,30078
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  gwaslab/ldsc_sumstats.py,sha256=O0olsDxKlh1MJ1gAuEN1t40rxhajOEwOQ20ak7xoDrI,26245
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  gwaslab/qc_check_datatype.py,sha256=kW68uk4dTLOU2b1dHoVat6n0loundDysAjIqxsXW28Q,3379
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- gwaslab/qc_fix_sumstats.py,sha256=rb1Iv05o0tYGGTiXXXJphkx-xVQNKAtlwkDfY-D0yPs,97979
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+ gwaslab/qc_fix_sumstats.py,sha256=u0YfC70zop2roUfq6mLMNL49m8AHPF2G-j8dKqW25yY,98261
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  gwaslab/run_script.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  gwaslab/util_abf_finemapping.py,sha256=LRcopjtkT-iXtKPAJIzR4qjPdhD7nrS_BGit4EW89FM,3054
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  gwaslab/util_ex_calculate_ldmatrix.py,sha256=Z_spxbq6SHDS0v84I59YTTF40iyLQIOZbt0dmEcNJjw,15417
@@ -53,23 +54,25 @@ gwaslab/util_in_get_density.py,sha256=kpKXH69acMkeYVG5vs-VbJC3COhmuLBfYco-wuOxgj
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  gwaslab/util_in_get_sig.py,sha256=53NOh7KueLY3vJPTNhhb37KPAIgLEfcP3k2zIV61lc4,39845
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  gwaslab/util_in_meta.py,sha256=5K9lIZcIgUy0AERqHy1GvMN2X6dp45JUUgopuDLgt4o,11284
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  gwaslab/util_in_snphwe.py,sha256=-KpIDx6vn_nah6H55IkV2OyjXQVXV13XyBL069WE1wM,1751
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- gwaslab/viz_aux_annotate_plot.py,sha256=i-Fvg_4H6LZvENM6F_yH9-sVSxjD_9LwVhlvgHusW6w,25006
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+ gwaslab/vis_plot_credible sets.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ gwaslab/viz_aux_annotate_plot.py,sha256=gA-s8a90dsl3MB5CIapdI_DecD9h2FmuqMgy07kMYJI,25207
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  gwaslab/viz_aux_chromatin.py,sha256=7cGmej5EkKO7fxR1b5w8r1oRRl9ofVzFRG52SCYWtz0,4109
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+ gwaslab/viz_aux_property.py,sha256=UIaivghnLXYpTwkKnXRK0F28Jbn9L6OaICk3K73WZaU,33
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  gwaslab/viz_aux_quickfix.py,sha256=HnhVvY0GP0EN0gLJ-B11OYiE5PWDcdKGUpQ3QZeu0lE,18592
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  gwaslab/viz_aux_reposition_text.py,sha256=iRIP-Rkltlei068HekJcVubiqPrunBqvAoSQ1eHk04M,4304
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  gwaslab/viz_aux_save_figure.py,sha256=GdUXNBOelsWqtTXm8pEZzeGGwDxHYnBkyrGwLOK16ew,2723
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  gwaslab/viz_plot_compare_af.py,sha256=qtXW45-Sq_ugK8ZfqBYMpmf58SKi3lB3YyHnzn_akcE,5344
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- gwaslab/viz_plot_compare_effect.py,sha256=60KlfRGj1TSc0-NCaInZ7GMiAUveXe4qDCjIW-RHJNE,51304
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+ gwaslab/viz_plot_compare_effect.py,sha256=kq-rVWygHEeTBMOtd_jk8nK85ClZHU-ADSf4nI2gTKo,66604
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  gwaslab/viz_plot_forestplot.py,sha256=xgOnefh737CgdQxu5naVyRNBX1NQXPFKzf51fbh6afs,6771
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  gwaslab/viz_plot_miamiplot.py,sha256=rCFEp7VNuVqeBBG3WRkmFAtFklbF79BvIQQYiSY70VY,31238
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  gwaslab/viz_plot_miamiplot2.py,sha256=xiFCgFX8hEySmCJORpEurMVER9eEXQyy_Ik7mLkbi9g,16015
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- gwaslab/viz_plot_mqqplot.py,sha256=nIwS3fMAXv_LVn7l9koSFZiZbcKCyuVq6Qg5fMzrEps,67049
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- gwaslab/viz_plot_phe_heatmap.py,sha256=vCCPAiTyBBVklZahXG_zmyxXPgm0d7ArVha7A6gJaok,9514
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+ gwaslab/viz_plot_mqqplot.py,sha256=emyEXZZenzm8eh3XFCkTWI8sz0fEnL5QJxohOZMxWZc,67189
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+ gwaslab/viz_plot_phe_heatmap.py,sha256=qoXVeFTIm-n8IinNbDdPFVBSz2yGCGK6QzTstXv6aj4,9532
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  gwaslab/viz_plot_qqplot.py,sha256=psQgVpP29686CEZkzQz0iRbApzqy7aE3GGiBcazVvNw,7247
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  gwaslab/viz_plot_regional2.py,sha256=tBoGox-4ngL5o_twdIjk_VW6Iam3JDyrPKuttm6_4Sg,36862
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  gwaslab/viz_plot_regionalplot.py,sha256=8u-5-yfy-UaXhaxVVz3Y5k2kBAoqzczUw1hyyD450iI,37983
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  gwaslab/viz_plot_rg_heatmap.py,sha256=PidUsgOiEVt6MfBPCF3_yDhOEytZ-I1q-ZD6_0pFrV4,13713
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- gwaslab/viz_plot_stackedregional.py,sha256=IRugpwLjqKdwuSVTQtCM36Rk4Gpv6MxdsGIWVj6vk8w,16651
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+ gwaslab/viz_plot_stackedregional.py,sha256=HfNUhwxevbwSoauE0ysG020U7YFVy4111nkIWdaJ4Q8,16664
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  gwaslab/viz_plot_trumpetplot.py,sha256=ZHdc6WcVx0-oKoj88yglRkmB4bS9pOiEMcuwKW35Yvo,42672
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  gwaslab/data/formatbook.json,sha256=N2nJs80HH98Rsu9FxaSvIQO9J5yIV97WEtAKjRqYwiY,38207
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  gwaslab/data/reference.json,sha256=IrjwFnXjrpVUp3zYfcYClpibJE9Y-94gtrC1Aw8sXxg,12332
@@ -79,9 +82,9 @@ gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz,sha256=qD9RsC5S2h6l-OdpW
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  gwaslab/data/hapmap3_SNPs/hapmap3_db151_hg38.snplist.gz,sha256=Y8ZT2FIAhbhlgCJdE9qQVAiwnV_fcsPt72usBa7RSBM,10225828
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  gwaslab/data/high_ld/high_ld_hla_hg19.bed.gz,sha256=R7IkssKu0L4WwkU9SrS84xCMdrkkKL0gnTNO_OKbG0Y,219
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  gwaslab/data/high_ld/high_ld_hla_hg38.bed.gz,sha256=76CIU0pibDJ72Y6UY-TbIKE9gEPwTELAaIbCXyjm80Q,470
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- gwaslab-3.5.0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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- gwaslab-3.5.0.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
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- gwaslab-3.5.0.dist-info/METADATA,sha256=SocHVFBOrjeEchxsvVLUgI4CZPwSypppxfSE7o7yp1I,7751
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- gwaslab-3.5.0.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
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- gwaslab-3.5.0.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
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- gwaslab-3.5.0.dist-info/RECORD,,
85
+ gwaslab-3.5.1.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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+ gwaslab-3.5.1.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
87
+ gwaslab-3.5.1.dist-info/METADATA,sha256=Dqj65vurvDR3JCwlyCVnnfUS64cmN1vMJJjUTCm3xLI,7758
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+ gwaslab-3.5.1.dist-info/WHEEL,sha256=R06PA3UVYHThwHvxuRWMqaGcr-PuniXahwjmQRFMEkY,91
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+ gwaslab-3.5.1.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
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+ gwaslab-3.5.1.dist-info/RECORD,,
{gwaslab-3.5.0.dist-info → gwaslab-3.5.1.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: setuptools (75.2.0)
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+ Generator: setuptools (75.5.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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