gwaslab 3.6.6__py3-none-any.whl → 3.6.8__py3-none-any.whl

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,            
@@ -90,6 +100,8 @@ def mqqplot(insumstats,
           qq_scatter_args=None,
           qqscatterargs=None,
           qq_line_color = "grey",
+          qq_xlabels = None,
+          qq_xlim = None,
           # region
           region = None,
           region_title=None,
@@ -194,6 +206,8 @@ def mqqplot(insumstats,
           highlight_color="#CB132D",
           highlight_windowkb = 500,
           highlight_anno_args = None,
+          highlight_lim = None,
+          highlight_lim_mode = "absolute",
           pinpoint= None,
           pinpoint_color ="red",
           stratified=False,
@@ -521,6 +535,8 @@ def mqqplot(insumstats,
                                                     highlight=highlight, 
                                                     highlight_chrpos=highlight_chrpos, 
                                                     highlight_windowkb=highlight_windowkb, 
+                                                    highlight_lim = highlight_lim, 
+                                                    highlight_lim_mode = highlight_lim_mode,
                                                     snpid=snpid, 
                                                     chrom=chrom, 
                                                     pos=pos)
@@ -1086,6 +1102,8 @@ def mqqplot(insumstats,
                     linewidth=sc_linewidth,
                     ytick3 = ytick3,
                     ylabels = ylabels,
+                    xlabels = qq_xlabels,
+                    xlim = qq_xlim,
                     ylabels_converted = ylabels_converted,
                     verbose=verbose,
                     qq_scatter_args=qq_scatter_args,
@@ -1325,19 +1343,38 @@ def _process_p_value(sumstats, mode,p, mlog10p, scaled, log, verbose ):
 
     return sumstats
 
-def _process_highlight(sumstats, highlight, highlight_chrpos, highlight_windowkb, snpid, chrom, pos):
+def _process_highlight(sumstats, highlight, highlight_chrpos, highlight_windowkb,  highlight_lim,  highlight_lim_mode, snpid, chrom, pos):
         if pd.api.types.is_list_like(highlight[0]):
             if highlight_chrpos == False:
                 # highlight for multiple sets
                 for i, highlight_set in enumerate(highlight):
                     to_highlight = sumstats.loc[sumstats[snpid].isin(highlight_set),:]
                     #assign colors: 0 is hightlight color
-                    for index,row in to_highlight.iterrows():
+                    #assign colors: i is highlight color
+                    for j, (index, row) in enumerate(to_highlight.iterrows()):
                         target_chr = int(row[chrom])
                         target_pos = int(row[pos])
                         right_chr=sumstats[chrom]==target_chr
-                        up_pos=sumstats[pos]>target_pos-highlight_windowkb*1000
-                        low_pos=sumstats[pos]<target_pos+highlight_windowkb*1000
+                        # Check if highlight_lim is provided for this group and SNP
+                        if (highlight_lim is not None and 
+                            i < len(highlight_lim) and 
+                            j < len(highlight_lim[i]) and 
+                            highlight_lim[i][j] is not None):
+                            # Use custom limits for this SNP
+                            if highlight_lim_mode == "absolute":
+                                # Absolute positions: (start_pos, end_pos)
+                                start_pos, end_pos = highlight_lim[i][j]
+                                up_pos = sumstats[pos] >= start_pos
+                                low_pos = sumstats[pos] <= end_pos
+                            else:
+                                # Offset mode: (lower_kb, upper_kb) relative to SNP position
+                                lower_kb, upper_kb = highlight_lim[i][j]
+                                up_pos = sumstats[pos] > target_pos + lower_kb * 1000
+                                low_pos = sumstats[pos] < target_pos + upper_kb * 1000
+                        else:
+                            # Use default highlight_windowkb
+                            up_pos = sumstats[pos] > target_pos - highlight_windowkb * 1000
+                            low_pos = sumstats[pos] < target_pos + highlight_windowkb * 1000
                         sumstats.loc[right_chr&up_pos&low_pos,"HUE"]=i
             else:
                 for i, highlight_chrpos_tuple in enumerate(highlight):
@@ -1361,13 +1398,30 @@ def _process_highlight(sumstats, highlight, highlight_chrpos, highlight_windowkb
         else:
             # highlight for one set
             to_highlight = sumstats.loc[sumstats[snpid].isin(highlight),:]
-            #assign colors: 0 is hightlight color
-            for index,row in to_highlight.iterrows():
+            #assign colors: 0 is highlight color
+            for j, (index, row) in enumerate(to_highlight.iterrows()):
                 target_chr = int(row[chrom])
                 target_pos = int(row[pos])
                 right_chr=sumstats[chrom]==target_chr
-                up_pos=sumstats[pos]>target_pos-highlight_windowkb*1000
-                low_pos=sumstats[pos]<target_pos+highlight_windowkb*1000
+                # Check if highlight_lim is provided for this SNP
+                if (highlight_lim is not None and 
+                    j < len(highlight_lim) and 
+                    highlight_lim[j] is not None):
+                    # Use custom limits for this SNP
+                    if highlight_lim_mode == "absolute":
+                        # Absolute positions: (start_pos, end_pos)
+                        start_pos, end_pos = highlight_lim[j]
+                        up_pos = sumstats[pos] >= start_pos
+                        low_pos = sumstats[pos] <= end_pos
+                    else:
+                        # Offset mode: (lower_kb, upper_kb) relative to SNP position
+                        lower_kb, upper_kb = highlight_lim[j]
+                        up_pos = sumstats[pos] > target_pos + lower_kb * 1000
+                        low_pos = sumstats[pos] < target_pos + upper_kb * 1000
+                else:
+                    # Use default highlight_windowkb
+                    up_pos = sumstats[pos] > target_pos - highlight_windowkb * 1000
+                    low_pos = sumstats[pos] < target_pos + highlight_windowkb * 1000
                 sumstats.loc[right_chr&up_pos&low_pos,"HUE"]=0
         return sumstats
 

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,
@@ -37,6 +39,8 @@ def _plot_qq(
     linewidth,
     ytick3,
     ylabels,
+    xlabels,
+    xlim,
     ylabels_converted,
     qq_scatter_args,
     expected_min_mlog10p,
@@ -153,32 +157,12 @@ def _plot_qq(
                         log=log,
                         verbose=verbose
                         )
-
-    #if cut == 0: 
-    #    ax2.set_ylim(skip, ceil(maxy*1.2) )
-    #    
-    #if cut:
-    #    qcutline = ax2.axhline(y=cut, linewidth = linewidth, linestyle="--",color=cut_line_color,zorder=1)
-    #    step=2
-    #    if ((maxticker-cut)/cutfactor + cut) > cut:
-    #        if ystep == 0:
-    #            if (cut - skip ) // step > 10:
-    #                step = (cut - skip ) // 10
-    #        else:
-    #            step = ystep
-#
-    #        ax2.set_yticks([x for x in range(skip,cut-step,step)]+[cut]+[(maxticker-cut)/cutfactor + cut])
-    #        ax2.set_yticklabels([x for x in range(skip,cut-step,step)]+[cut]+[maxticker],fontsize=fontsize,family=font_family)
-    #    else:
-    #        if ystep == 0:
-    #            if (cut - skip ) // step > 10:
-    #                step = (cut - skip ) // 10
-    #        else:
-    #            step = ystep
-#
-    #        ax2.set_yticks([x for x in range(skip,cut-step,step)]+[cut])
-    #        ax2.set_yticklabels([x for x in range(skip,cut-step,step)]+[cut],fontsize=fontsize,family=font_family)
-    #    ax2.set_ylim(bottom = skip)
+    if xlim is not None:
+        ax2.set_xlim(xlim)
+        
+    if xlabels is not None:
+        ax2.set_xticks(xlabels)
+        ax2.set_xticklabels(xlabels,fontsize=fontsize,family=font_family)
 
     ax2.tick_params(axis='both', which='both', labelsize=fontsize,labelfontfamily=font_family)
     #

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,

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

@@ -16,11 +16,12 @@ 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 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,