gwaslab 3.6.5__py3-none-any.whl → 3.6.7__py3-none-any.whl

gwaslab/{util_in_get_sig.py → util/util_in_get_sig.py}

@@ -5,20 +5,22 @@ import gc
 from pyensembl import EnsemblRelease
 from pyensembl import Genome
 from os import path
-from gwaslab.util_in_fill_data import fill_p
 from gwaslab.g_Log import Log
-from gwaslab.bd_common_data import get_chr_to_number
-from gwaslab.bd_common_data import get_number_to_chr
-from gwaslab.bd_common_data import get_chr_to_NC
-from gwaslab.bd_common_data import gtf_to_protein_coding
-from gwaslab.bd_common_data import gtf_to_all_gene
-from gwaslab.bd_download import check_and_download
-from gwaslab.util_ex_gwascatalog import gwascatalog_trait
-from gwaslab.qc_fix_sumstats import check_dataframe_shape
-from gwaslab.qc_fix_sumstats import start_to
-from gwaslab.qc_fix_sumstats import finished
-from gwaslab.qc_build import _check_build
-from gwaslab.util_in_correct_winnerscurse import wc_correct
+
+from gwaslab.bd.bd_common_data import get_chr_to_number
+from gwaslab.bd.bd_common_data import get_number_to_chr
+from gwaslab.bd.bd_common_data import get_chr_to_NC
+from gwaslab.bd.bd_common_data import gtf_to_protein_coding
+from gwaslab.bd.bd_common_data import gtf_to_all_gene
+from gwaslab.bd.bd_download import check_and_download
+
+from gwaslab.qc.qc_fix_sumstats import check_dataframe_shape
+from gwaslab.qc.qc_fix_sumstats import start_to
+from gwaslab.qc.qc_fix_sumstats import finished
+from gwaslab.qc.qc_build import _check_build
+from gwaslab.util.util_in_correct_winnerscurse import wc_correct
+from gwaslab.util.util_ex_gwascatalog import gwascatalog_trait
+from gwaslab.util.util_in_fill_data import fill_p
 # getsig
 # closest_gene
 # annogene

gwaslab/{util_in_meta.py → util/util_in_meta.py}

@@ -4,7 +4,7 @@ import numpy as np
 from scipy.stats.distributions import chi2
 from scipy.stats import norm
 from gwaslab.g_Log import Log
-from gwaslab.io_to_pickle import load_data_from_pickle
+from gwaslab.io.io_to_pickle import load_data_from_pickle
 from gwaslab.g_Sumstats import Sumstats
 import gc
 

gwaslab/{util_in_meta_polars.py → util/util_in_meta_polars.py}

@@ -4,7 +4,7 @@ import numpy as np
 from scipy.stats.distributions import chi2
 from scipy.stats import norm
 from gwaslab.g_Log import Log
-from gwaslab.io_to_pickle import load_data_from_pickle
+from gwaslab.io.io_to_pickle import load_data_from_pickle
 from gwaslab.g_Sumstats import Sumstats
 import polars as pl
 ########################################################################################################################################################################################################################################################################################################################################################

gwaslab/{viz_aux_annotate_plot.py → viz/viz_aux_annotate_plot.py}

@@ -9,7 +9,7 @@ from scipy import stats
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 from adjustText import adjust_text
 from gwaslab.g_Log import Log
-from gwaslab.viz_aux_reposition_text import adjust_text_position
+from gwaslab.viz.viz_aux_reposition_text import adjust_text_position
 from pandas.api.types import is_string_dtype
 
 # single mqqplot

gwaslab/{viz_aux_quickfix.py → viz/viz_aux_quickfix.py}

@@ -3,8 +3,8 @@ import numpy as np
 from gwaslab.g_Log import Log
 from matplotlib import ticker
 import matplotlib.pyplot as plt
-from gwaslab.bd_common_data import get_chr_to_number
-from gwaslab.bd_common_data import get_number_to_chr
+from gwaslab.bd.bd_common_data import get_chr_to_number
+from gwaslab.bd.bd_common_data import get_number_to_chr
 from math import ceil
 
 def _quick_fix(sumstats, chr_dict=get_chr_to_number(), scaled=False, chrom="CHR", pos="POS", p="P", mlog10p="MLOG10P",log=Log(), verbose=True):

gwaslab/{viz_plot_compare_af.py → viz/viz_plot_compare_af.py}

@@ -4,7 +4,7 @@ import matplotlib.pyplot as plt
 import scipy.stats as ss
 import seaborn as sns
 from gwaslab.g_Log import Log
-from gwaslab.viz_aux_save_figure import save_figure
+from gwaslab.viz.viz_aux_save_figure import save_figure
 
 ################################################################################################################################
 def plotdaf(sumstats,

gwaslab/{viz_plot_compare_effect.py → viz/viz_plot_compare_effect.py}

@@ -8,15 +8,18 @@ import math
 import scipy.stats as ss
 from matplotlib.patches import Rectangle
 from adjustText import adjust_text
-from gwaslab.viz_aux_save_figure import save_figure
-from gwaslab.util_in_get_sig import getsig
-from gwaslab.util_in_get_sig import annogene
 from gwaslab.g_Log import Log
-from gwaslab.util_in_correct_winnerscurse import wc_correct
-from gwaslab.util_in_correct_winnerscurse import wc_correct_test
 from gwaslab.g_Sumstats import Sumstats
-from gwaslab.io_process_args import _merge_and_sync_dic
-from gwaslab.io_process_args import _extract_kwargs
+
+from gwaslab.viz.viz_aux_save_figure import save_figure
+
+from gwaslab.util.util_in_get_sig import getsig
+from gwaslab.util.util_in_get_sig import annogene
+from gwaslab.util.util_in_correct_winnerscurse import wc_correct
+from gwaslab.util.util_in_correct_winnerscurse import wc_correct_test
+
+from gwaslab.io.io_process_args import _merge_and_sync_dic
+from gwaslab.io.io_process_args import _extract_kwargs
 #20220422
 def compare_effect(path1,
                    path2,
@@ -91,13 +94,17 @@ def compare_effect(path1,
         exponent = math.floor(math.log10(sig_level))
         mantissa = sig_level / 10**exponent
 
-        legend_title =  '$\mathregular{ P < {} x 10^{{{}}}}$ in:'.format(mantissa, exponent)
+        legend_title =  '$\mathregular{{ P < {} x 10^{{{}}} }}$ in:'.format(mantissa, exponent)
 
+    # what method to use for correction
     if is_q_mc=="fdr" or is_q_mc=="bon":
         is_q = True
+
+    # if heterogeneity test
     if is_q == True:
         if is_q_mc not in [False,"fdr","bon","non"]:
             raise ValueError('Please select either "fdr" or "bon" or "non"/False for is_q_mc.')
+        
     if save_args is None:
         save_args = {"dpi":300,"facecolor":"white"}
     if reg_box is None:
@@ -985,6 +992,7 @@ def test_q(df,beta1,se1,beta2,se2,q_level=0.05,is_q_mc=False, log=Log(), verbose
         log.write(" -Bonferroni correction applied...", verbose=verbose)
         df[rawpq] = df[pq] 
         df[pq] = df[pq] * len(df[pq])
+        # P value upper bound -> 1
         df.loc[df[pq]>1,pq] = 1
 
     df.loc[df[pq]<q_level,"Edge_color"]="black"

gwaslab/{viz_plot_credible_sets.py → viz/viz_plot_credible_sets.py}

@@ -3,12 +3,12 @@ import matplotlib.pyplot as plt
 import pandas as pd
 import seaborn as sns
 from gwaslab.g_Log import Log
-from gwaslab.viz_aux_quickfix import _quick_assign_i_with_rank
-from gwaslab.viz_plot_mqqplot import _process_xtick
-from gwaslab.viz_plot_mqqplot import _process_xlabel
-from gwaslab.bd_common_data import get_number_to_chr
-from gwaslab.util_in_filter_value import _filter_region
-from gwaslab.io_process_args import _extract_kwargs
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_i_with_rank
+from gwaslab.viz.viz_plot_mqqplot import _process_xtick
+from gwaslab.viz.viz_plot_mqqplot import _process_xlabel
+from gwaslab.bd.bd_common_data import get_number_to_chr
+from gwaslab.util.util_in_filter_value import _filter_region
+from gwaslab.io.io_process_args import _extract_kwargs
 import copy
 
 def _plot_cs(pipcs_raw,

gwaslab/{viz_plot_effect.py → viz/viz_plot_effect.py}

@@ -1,62 +1,8 @@
 import pandas as pd
 import matplotlib.pyplot as plt
-import matplotlib.ticker as ticker
-import matplotlib.patches as patches
-import seaborn as sns
-import numpy as np
-import scipy as sp
-import copy
-from math import ceil
-from shutil import which
-from pyensembl import EnsemblRelease
-from allel import GenotypeArray
-from allel import read_vcf
-from allel import rogers_huff_r_between
-import matplotlib as mpl
-from scipy import stats
-from mpl_toolkits.axes_grid1.inset_locator import inset_axes
-from mpl_toolkits.axes_grid1.inset_locator import mark_inset
-from matplotlib.ticker import MaxNLocator
-import gc as garbage_collect
-from adjustText import adjust_text
-from gwaslab.viz_aux_reposition_text import adjust_text_position
-from gwaslab.viz_aux_annotate_plot import annotate_single
-from gwaslab.viz_plot_qqplot import _plot_qq
-from gwaslab.hm_harmonize_sumstats import auto_check_vcf_chr_dict
-from gwaslab.viz_plot_regional2 import _plot_regional
-from gwaslab.viz_plot_regional2 import process_vcf
-from gwaslab.viz_plot_regional2 import _get_lead_id
-from gwaslab.viz_aux_quickfix import _get_largenumber
-from gwaslab.viz_aux_quickfix import _quick_fix_p_value
-from gwaslab.viz_aux_quickfix import _quick_fix_pos
-from gwaslab.viz_aux_quickfix import _quick_fix_chr
-from gwaslab.viz_aux_quickfix import _quick_fix_eaf
-from gwaslab.viz_aux_quickfix import _quick_fix_mlog10p
-from gwaslab.viz_aux_quickfix import _quick_add_tchrpos
-from gwaslab.viz_aux_quickfix import _quick_merge_sumstats
-from gwaslab.viz_aux_quickfix import _quick_assign_i
-from gwaslab.viz_aux_quickfix import _quick_assign_i_with_rank
-from gwaslab.viz_aux_quickfix import _quick_extract_snp_in_region
-from gwaslab.viz_aux_quickfix import _quick_assign_highlight_hue_pair
-from gwaslab.viz_aux_quickfix import _quick_assign_marker_relative_size
-from gwaslab.viz_aux_quickfix import _cut
-from gwaslab.viz_aux_quickfix import _set_yticklabels
-from gwaslab.viz_aux_quickfix import _jagged_y
-from gwaslab.viz_aux_save_figure import save_figure
+from gwaslab.viz.viz_aux_save_figure import save_figure
 from gwaslab.g_Log import Log
-from gwaslab.util_in_calculate_gc import lambdaGC
-from gwaslab.util_in_get_sig import getsig
-from gwaslab.util_in_get_sig import annogene
-from gwaslab.bd_common_data import get_chr_to_number
-from gwaslab.bd_common_data import get_number_to_chr
-from gwaslab.bd_common_data import get_recombination_rate
-from gwaslab.bd_common_data import get_gtf
-from gwaslab.util_in_filter_value import _filter_region
-from gwaslab.g_version import _get_version
-from matplotlib.colors import ListedColormap
-from matplotlib.colors import LinearSegmentedColormap
-from matplotlib.colors import to_hex
-from gwaslab.io_process_args import _extract_kwargs
+from gwaslab.io.io_process_args import _extract_kwargs
 
 def _plot_effect(to_plot, 
                  y=None, 
@@ -82,15 +28,19 @@ def _plot_effect(to_plot,
                  effect_label=None,
                  eaf_label=None,
                  snpr2_label=None,
+                 xlim_eaf=None,
+                 xlim_snpr2 = None,
                  log=Log(),
                  verbose=True,
                  legend_mode=1,
                  ncol=2,
+                 gap=1,
                  fontsize=12,
                  font_family="Arial",
                  size=None,
                  hue=None,
                  style=None,
+                 sort_args=None,
                  **args):
 
     if err_args is None:
@@ -108,7 +58,8 @@ def _plot_effect(to_plot,
         fig_args={"figsize":(8,8),"dpi":300}
     if scatter_args is None:
         scatter_args={"s":20}
-    
+    if sort_args is None:
+        sort_args={}
 
     legend_titles=[]
     if hue is not None:
@@ -142,17 +93,24 @@ def _plot_effect(to_plot,
     if y_sort is None:
         y_sort = ["CHR","POS","STUDY"]
     
-    to_plot = to_plot.sort_values(by=y_sort)
+    #to_plot = to_plot.sort_values(by=y_sort)
 
     if group is None:
-        group = ["CHR","POS"]
-        to_plot = to_plot.sort_values(by=group)
-    # Assign group IDs based on the sorted 'score'
-        
-    to_plot['_VAR_GROUP'] = to_plot.groupby(group).ngroup() + 1
+        group = ["CHR","POS"] + y_sort
+    
+    sort_columns= group + y_sort
 
-    to_plot["_VAR_INDEX"] = range(len(to_plot))
-    to_plot["_VAR_INDEX"]= to_plot["_VAR_INDEX"] + to_plot['_VAR_GROUP']
+    to_plot = to_plot.sort_values(by=sort_columns,**sort_args)
+    
+    # calculate cum sum
+    cum_sizes = to_plot.groupby(group).size()
+    cum_sizes = cum_sizes +  gap 
+    cum_sizes = cum_sizes.cumsum() 
+    
+    # create index for y axis
+    to_plot['_GROUP_CUMSUM'] = to_plot.set_index(group).index.map(cum_sizes)
+    to_plot['_VAR_INDEX'] = to_plot.groupby(group).cumcount()
+    to_plot["_VAR_INDEX"]=  to_plot['_GROUP_CUMSUM'] - to_plot['_VAR_INDEX'] 
 
     y="_VAR_INDEX"
 
@@ -171,15 +129,15 @@ def _plot_effect(to_plot,
         fig,ax1 = plt.subplots(ncols=ncols, **fig_args)
     elif ncols==2:
         if eaf_panel==True:
-            fig,axes = plt.subplots(ncols=ncols, dpi=400,sharey=True)
+            fig,axes = plt.subplots(ncols=ncols, dpi=400,sharey=True, **fig_args)
             ax1=axes[0]
             ax2=axes[1]
         else:
-            fig,axes = plt.subplots(ncols=ncols, dpi=400,sharey=True)
+            fig,axes = plt.subplots(ncols=ncols, dpi=400,sharey=True, **fig_args)
             ax1=axes[0]
             ax3=axes[1]
     else:
-        fig,axes = plt.subplots(ncols=ncols, dpi=400,sharey=True)
+        fig,axes = plt.subplots(ncols=ncols, dpi=400,sharey=True, **fig_args)
         ax1=axes[0]
         ax2=axes[1]
         ax3=axes[2]
@@ -192,6 +150,7 @@ def _plot_effect(to_plot,
     ax1.axvline(x=0,linestyle="dashed",c="grey")
     ax1.set_yticks(to_plot[y], labels = to_plot[y_name], fontsize=fontsize, family=font_family)
     ax1.set_ylabel(ylabel, fontsize=fontsize, family=font_family) 
+    ax1.set_xlabel(x, fontsize=fontsize, family=font_family) 
 
     if title is not None:
         ax1.set_title(title,fontsize=fontsize, family=font_family)
@@ -199,11 +158,14 @@ def _plot_effect(to_plot,
     if eaf_panel==True:
         ax2.barh(y=to_plot[y], width=to_plot[eaf], zorder=100, **eaf_args)
         ax2.set_xlabel(eaf, fontsize=fontsize, family=font_family)
+        if xlim_eaf is not None:
+            ax3.set_xlim(xlim_eaf)
 
     if snpvar_panel==True:
         ax3.barh(y=to_plot[y], width=to_plot[snpr2], zorder=100,**snpr2_args)
         ax3.set_xlabel(snpr2, fontsize=fontsize, family=font_family)
-    
+        if xlim_snpr2 is not None:
+            ax3.set_xlim(xlim_snpr2)
     #try:
     if legend_mode==1:
         #if ncols==1:
@@ -273,6 +235,12 @@ def _plot_effect(to_plot,
     #    for legend_row in legend_rows[:-1]:
     #        ax1.add_artist(legend_row)
 
+
+
+    ax1.tick_params(axis='x', 
+                        labelsize=fontsize,
+                        labelfontfamily=font_family) 
+    
     if effect_label is not None:
         ax1.set_xlabel(effect_label, fontsize=fontsize, family=font_family)
         ax1.tick_params(axis='x', 

gwaslab/{viz_plot_miamiplot.py → viz/viz_plot_miamiplot.py}

@@ -14,32 +14,40 @@ from scipy import stats
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 import gc as garbage_collect
 from adjustText import adjust_text
+
+from gwaslab.g_Sumstats import Sumstats
 from gwaslab.g_Log import Log
-from gwaslab.util_in_get_sig import getsig
-from gwaslab.util_in_get_sig import annogene
-from gwaslab.bd_common_data import get_chr_to_number
-from gwaslab.bd_common_data import get_number_to_chr
-from gwaslab.bd_common_data import get_recombination_rate
-from gwaslab.bd_common_data import get_gtf
-from gwaslab.viz_aux_reposition_text import adjust_text_position
-from gwaslab.viz_aux_quickfix import _quick_fix
+
+from gwaslab.util.util_in_get_sig import getsig
+from gwaslab.util.util_in_get_sig import annogene
+
+from gwaslab.bd.bd_common_data import get_chr_to_number
+from gwaslab.bd.bd_common_data import get_number_to_chr
+from gwaslab.bd.bd_common_data import get_recombination_rate
+from gwaslab.bd.bd_common_data import get_gtf
+
+
 #from gwaslab.quickfix import _quick_fix_p
 #from gwaslab.quickfix import _quick_fix_mlog10p
 #from gwaslab.quickfix import _quick_fix_chr
 #from gwaslab.quickfix import _quick_fix_pos
 #from gwaslab.quickfix import _quick_fix_eaf
-from gwaslab.viz_aux_quickfix import _get_largenumber
-from gwaslab.viz_aux_quickfix import _quick_add_tchrpos
-from gwaslab.viz_aux_quickfix import _quick_merge_sumstats
-from gwaslab.viz_aux_quickfix import _quick_assign_i
-from gwaslab.viz_aux_quickfix import _quick_extract_snp_in_region
-from gwaslab.viz_aux_quickfix import _quick_assign_highlight_hue_pair
-from gwaslab.viz_aux_quickfix import _quick_assign_marker_relative_size
-from gwaslab.viz_aux_annotate_plot import annotate_pair
-from gwaslab.io_to_pickle import load_pickle
-from gwaslab.io_to_pickle import load_data_from_pickle
-from gwaslab.g_Sumstats import Sumstats
-from gwaslab.viz_aux_save_figure import save_figure
+from gwaslab.viz.viz_aux_reposition_text import adjust_text_position
+from gwaslab.viz.viz_aux_quickfix import _quick_fix
+from gwaslab.viz.viz_aux_quickfix import _get_largenumber
+from gwaslab.viz.viz_aux_quickfix import _quick_add_tchrpos
+from gwaslab.viz.viz_aux_quickfix import _quick_merge_sumstats
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_i
+from gwaslab.viz.viz_aux_quickfix import _quick_extract_snp_in_region
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_highlight_hue_pair
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_marker_relative_size
+from gwaslab.viz.viz_aux_annotate_plot import annotate_pair
+from gwaslab.viz.viz_aux_save_figure import save_figure
+
+from gwaslab.io.io_to_pickle import load_pickle
+from gwaslab.io.io_to_pickle import load_data_from_pickle
+
+
 
 def plot_miami( 
           path1,

gwaslab/{viz_plot_miamiplot2.py → viz/viz_plot_miamiplot2.py}

@@ -14,30 +14,35 @@ from scipy import stats
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 import gc as garbage_collect
 from adjustText import adjust_text
+
 from gwaslab.g_Log import Log
-from gwaslab.util_in_get_sig import getsig
-from gwaslab.util_in_get_sig import annogene
-from gwaslab.bd_common_data import get_chr_to_number
-from gwaslab.bd_common_data import get_number_to_chr
-from gwaslab.bd_common_data import get_recombination_rate
-from gwaslab.bd_common_data import get_gtf
-from gwaslab.viz_aux_reposition_text import adjust_text_position
-from gwaslab.viz_aux_quickfix import _quick_fix
-from gwaslab.viz_aux_quickfix import _get_largenumber
-from gwaslab.viz_aux_quickfix import _quick_add_tchrpos
-from gwaslab.viz_aux_quickfix import _quick_merge_sumstats
-from gwaslab.viz_aux_quickfix import _quick_assign_i
-from gwaslab.viz_aux_quickfix import _quick_assign_i_with_rank
-from gwaslab.viz_aux_quickfix import _quick_extract_snp_in_region
-from gwaslab.viz_aux_quickfix import _quick_assign_highlight_hue_pair
-from gwaslab.viz_aux_quickfix import _quick_assign_marker_relative_size
-from gwaslab.viz_aux_annotate_plot import annotate_pair
-from gwaslab.io_to_pickle import load_pickle
-from gwaslab.io_to_pickle import load_data_from_pickle
-from gwaslab.g_Sumstats import Sumstats
-from gwaslab.viz_aux_save_figure import save_figure
-from gwaslab.viz_plot_mqqplot import mqqplot
 from gwaslab.g_version import _get_version
+from gwaslab.g_Sumstats import Sumstats
+
+from gwaslab.util.util_in_get_sig import getsig
+from gwaslab.util.util_in_get_sig import annogene
+
+from gwaslab.bd.bd_common_data import get_chr_to_number
+from gwaslab.bd.bd_common_data import get_number_to_chr
+from gwaslab.bd.bd_common_data import get_recombination_rate
+from gwaslab.bd.bd_common_data import get_gtf
+
+from gwaslab.viz.viz_aux_reposition_text import adjust_text_position
+from gwaslab.viz.viz_aux_quickfix import _quick_fix
+from gwaslab.viz.viz_aux_quickfix import _get_largenumber
+from gwaslab.viz.viz_aux_quickfix import _quick_add_tchrpos
+from gwaslab.viz.viz_aux_quickfix import _quick_merge_sumstats
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_i
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_i_with_rank
+from gwaslab.viz.viz_aux_quickfix import _quick_extract_snp_in_region
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_highlight_hue_pair
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_marker_relative_size
+from gwaslab.viz.viz_aux_annotate_plot import annotate_pair
+from gwaslab.viz.viz_aux_save_figure import save_figure
+from gwaslab.viz.viz_plot_mqqplot import mqqplot
+
+from gwaslab.io.io_to_pickle import load_pickle
+from gwaslab.io.io_to_pickle import load_data_from_pickle
 
 def plot_miami2( 
           path1=None,

gwaslab/{viz_plot_mqqplot.py → viz/viz_plot_mqqplot.py}

@@ -2,6 +2,10 @@ import pandas as pd
 import matplotlib.pyplot as plt
 import matplotlib.ticker as ticker
 import matplotlib.patches as patches
+from matplotlib.colors import ListedColormap
+from matplotlib.colors import LinearSegmentedColormap
+from matplotlib.colors import to_hex
+
 import seaborn as sns
 import numpy as np
 import scipy as sp
@@ -19,46 +23,52 @@ from mpl_toolkits.axes_grid1.inset_locator import mark_inset
 from matplotlib.ticker import MaxNLocator
 import gc as garbage_collect
 from adjustText import adjust_text
-from gwaslab.viz_aux_reposition_text import adjust_text_position
-from gwaslab.viz_aux_annotate_plot import annotate_single
-from gwaslab.viz_plot_qqplot import _plot_qq
-from gwaslab.hm_harmonize_sumstats import auto_check_vcf_chr_dict
-from gwaslab.viz_plot_regional2 import _plot_regional
-from gwaslab.viz_plot_regional2 import process_vcf
-from gwaslab.io_load_ld import process_ld
-from gwaslab.viz_plot_regional2 import _get_lead_id
-from gwaslab.viz_aux_quickfix import _get_largenumber
-from gwaslab.viz_aux_quickfix import _quick_fix_p_value
-from gwaslab.viz_aux_quickfix import _quick_fix_pos
-from gwaslab.viz_aux_quickfix import _quick_fix_chr
-from gwaslab.viz_aux_quickfix import _quick_fix_eaf
-from gwaslab.viz_aux_quickfix import _quick_fix_mlog10p
-from gwaslab.viz_aux_quickfix import _quick_add_tchrpos
-from gwaslab.viz_aux_quickfix import _quick_merge_sumstats
-from gwaslab.viz_aux_quickfix import _quick_assign_i
-from gwaslab.viz_aux_quickfix import _quick_assign_i_with_rank
-from gwaslab.viz_aux_quickfix import _quick_extract_snp_in_region
-from gwaslab.viz_aux_quickfix import _quick_assign_highlight_hue_pair
-from gwaslab.viz_aux_quickfix import _quick_assign_marker_relative_size
-from gwaslab.viz_aux_quickfix import _cut
-from gwaslab.viz_aux_quickfix import _set_yticklabels
-from gwaslab.viz_aux_quickfix import _jagged_y
-from gwaslab.io_process_args import _update_args
-from gwaslab.io_process_args import _update_arg
-from gwaslab.viz_aux_save_figure import save_figure
+
 from gwaslab.g_Log import Log
-from gwaslab.util_in_calculate_gc import lambdaGC
-from gwaslab.util_in_get_sig import getsig
-from gwaslab.util_in_get_sig import annogene
-from gwaslab.bd_common_data import get_chr_to_number
-from gwaslab.bd_common_data import get_number_to_chr
-from gwaslab.bd_common_data import get_recombination_rate
-from gwaslab.bd_common_data import get_gtf
-from gwaslab.util_in_filter_value import _filter_region
 from gwaslab.g_version import _get_version
-from matplotlib.colors import ListedColormap
-from matplotlib.colors import LinearSegmentedColormap
-from matplotlib.colors import to_hex
+
+from gwaslab.hm.hm_harmonize_sumstats import auto_check_vcf_chr_dict
+
+from gwaslab.viz.viz_aux_reposition_text import adjust_text_position
+from gwaslab.viz.viz_aux_annotate_plot import annotate_single
+from gwaslab.viz.viz_plot_qqplot import _plot_qq
+from gwaslab.viz.viz_plot_regional2 import _plot_regional
+from gwaslab.viz.viz_plot_regional2 import process_vcf
+from gwaslab.viz.viz_plot_regional2 import _get_lead_id
+from gwaslab.viz.viz_aux_quickfix import _get_largenumber
+from gwaslab.viz.viz_aux_quickfix import _quick_fix_p_value
+from gwaslab.viz.viz_aux_quickfix import _quick_fix_pos
+from gwaslab.viz.viz_aux_quickfix import _quick_fix_chr
+from gwaslab.viz.viz_aux_quickfix import _quick_fix_eaf
+from gwaslab.viz.viz_aux_quickfix import _quick_fix_mlog10p
+from gwaslab.viz.viz_aux_quickfix import _quick_add_tchrpos
+from gwaslab.viz.viz_aux_quickfix import _quick_merge_sumstats
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_i
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_i_with_rank
+from gwaslab.viz.viz_aux_quickfix import _quick_extract_snp_in_region
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_highlight_hue_pair
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_marker_relative_size
+from gwaslab.viz.viz_aux_quickfix import _cut
+from gwaslab.viz.viz_aux_quickfix import _set_yticklabels
+from gwaslab.viz.viz_aux_quickfix import _jagged_y
+from gwaslab.viz.viz_aux_save_figure import save_figure
+
+from gwaslab.io.io_load_ld import process_ld
+from gwaslab.io.io_process_args import _update_args
+from gwaslab.io.io_process_args import _update_arg
+
+from gwaslab.util.util_in_filter_value import _filter_region
+from gwaslab.util.util_in_calculate_gc import lambdaGC
+from gwaslab.util.util_in_get_sig import getsig
+from gwaslab.util.util_in_get_sig import annogene
+
+from gwaslab.bd.bd_common_data import get_chr_to_number
+from gwaslab.bd.bd_common_data import get_number_to_chr
+from gwaslab.bd.bd_common_data import get_recombination_rate
+from gwaslab.bd.bd_common_data import get_gtf
+
+
+
 # 20230202 ######################################################################################################
 
 def mqqplot(insumstats,            

gwaslab/{viz_plot_phe_heatmap.py → viz/viz_plot_phe_heatmap.py}

@@ -3,24 +3,27 @@ import matplotlib.pyplot as plt
 import seaborn as sns
 import numpy as np
 import scipy as sp
-from gwaslab.viz_aux_quickfix import _quick_assign_i_with_rank
-from gwaslab.viz_aux_quickfix import _get_largenumber
-from gwaslab.viz_aux_quickfix import _quick_fix_p_value
-from gwaslab.viz_aux_quickfix import _quick_fix_pos
-from gwaslab.viz_aux_quickfix import _quick_fix_chr
-from gwaslab.viz_aux_quickfix import _quick_fix_eaf
-from gwaslab.viz_aux_quickfix import _quick_fix_mlog10p
-from gwaslab.viz_aux_quickfix import _dropna_in_cols
-from gwaslab.viz_plot_mqqplot import _process_p_value
-from gwaslab.viz_plot_mqqplot import _configure_fig_save_kwargs
-from gwaslab.viz_plot_mqqplot import mqqplot
-from gwaslab.viz_aux_save_figure import save_figure
-from gwaslab.g_Log import Log
 import copy
-from gwaslab.bd_common_data import get_chr_to_number
-from gwaslab.bd_common_data import get_number_to_chr
+from gwaslab.g_Log import Log
 from gwaslab.g_version import _get_version
 
+from gwaslab.viz.viz_aux_quickfix import _quick_assign_i_with_rank
+from gwaslab.viz.viz_aux_quickfix import _get_largenumber
+from gwaslab.viz.viz_aux_quickfix import _quick_fix_p_value
+from gwaslab.viz.viz_aux_quickfix import _quick_fix_pos
+from gwaslab.viz.viz_aux_quickfix import _quick_fix_chr
+from gwaslab.viz.viz_aux_quickfix import _quick_fix_eaf
+from gwaslab.viz.viz_aux_quickfix import _quick_fix_mlog10p
+from gwaslab.viz.viz_aux_quickfix import _dropna_in_cols
+from gwaslab.viz.viz_plot_mqqplot import _process_p_value
+from gwaslab.viz.viz_plot_mqqplot import _configure_fig_save_kwargs
+from gwaslab.viz.viz_plot_mqqplot import mqqplot
+from gwaslab.viz.viz_aux_save_figure import save_figure
+
+from gwaslab.bd.bd_common_data import get_chr_to_number
+from gwaslab.bd.bd_common_data import get_number_to_chr
+
+
 def _gwheatmap(
     insumstats,    
     chrom="CHR",

gwaslab/{viz_plot_qqplot.py → viz/viz_plot_qqplot.py}

@@ -4,9 +4,11 @@ import seaborn as sns
 import numpy as np
 import scipy as sp
 from math import ceil
-from gwaslab.viz_aux_quickfix import _set_yticklabels
 from gwaslab.g_Log import Log
-from gwaslab.util_in_calculate_gc import lambdaGC
+
+from gwaslab.viz.viz_aux_quickfix import _set_yticklabels
+from gwaslab.util.util_in_calculate_gc import lambdaGC
+
 # qq plot module for mqqplot
 def _plot_qq(
     sumstats,

gwaslab/{viz_plot_regional2.py → viz/viz_plot_regional2.py}

@@ -2,6 +2,11 @@ import pandas as pd
 import matplotlib.pyplot as plt
 import matplotlib.ticker as ticker
 import matplotlib.patches as patches
+from matplotlib.colors import ListedColormap
+from matplotlib.colors import LinearSegmentedColormap
+import matplotlib.colors
+from matplotlib.colors import Normalize
+from matplotlib.patches import Rectangle
 import seaborn as sns
 import numpy as np
 import copy
@@ -17,16 +22,13 @@ from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 from mpl_toolkits.axes_grid1.inset_locator import mark_inset
 from adjustText import adjust_text
 from gtfparse import read_gtf
+
 from gwaslab.g_Log import Log
-from gwaslab.bd_common_data import get_chr_to_number
-from gwaslab.bd_common_data import get_number_to_chr
-from gwaslab.bd_common_data import get_recombination_rate
-from gwaslab.bd_common_data import get_gtf
-from matplotlib.colors import ListedColormap
-from matplotlib.colors import LinearSegmentedColormap
-import matplotlib.colors
-from matplotlib.colors import Normalize
-from matplotlib.patches import Rectangle
+from gwaslab.bd.bd_common_data import get_chr_to_number
+from gwaslab.bd.bd_common_data import get_number_to_chr
+from gwaslab.bd.bd_common_data import get_recombination_rate
+from gwaslab.bd.bd_common_data import get_gtf
+
 
 def _plot_regional(
     sumstats,