gwaslab 3.4.37__py3-none-any.whl → 3.4.39__py3-none-any.whl

gwaslab/viz_aux_annotate_plot.py

@@ -58,7 +58,7 @@ def annotate_single(
                 annotation_col="CHR:POS"
         elif anno:
                 annotation_col=anno
-        if verbose: log.write(" -Annotating using column "+annotation_col+"...")
+        log.write(" -Annotating using column "+annotation_col+"...", verbose=verbose)
         
         ## calculate y span
         if region is not None:
@@ -66,7 +66,7 @@ def annotate_single(
         else:
             y_span = sumstats["i"].max()-sumstats["i"].min()
         
-        if verbose: log.write(" -Adjusting text positions with repel_force={}...".format(repel_force))
+        log.write(" -Adjusting text positions with repel_force={}...".format(repel_force), verbose=verbose)
         if anno_style == "expand" :
             to_annotate.loc[:, "ADJUSTED_i"] = adjust_text_position(to_annotate["i"].values.copy(), y_span, repel_force,max_iter=anno_max_iter,log=log,amode=amode,verbose=verbose)
         ##  iterate through variants to be annotated
@@ -214,7 +214,7 @@ def annotate_single(
             anno_count +=1
         #anno_adjust_keyargs = {"arrowprops":dict(arrowstyle='->', color='grey', linewidth=0.1,relpos=(0.5,0.5))}
         if anno_adjust==True:
-            if verbose: log.write(" -Auto-adjusting text positions...")
+            log.write(" -Auto-adjusting text positions...", verbose=verbose)
             adjust_text(texts = anno_to_adjust_list,
                         autoalign=False, 
                         only_move={'points':'x', 'text':'x', 'objects':'x'},
@@ -232,7 +232,7 @@ def annotate_single(
                         )
         
     else:
-        if verbose: log.write(" -Skip annotating")
+        log.write(" -Skip annotating", verbose=verbose)
     
     return ax1
 
@@ -275,7 +275,7 @@ def annotate_pair(
         for index,ax,to_annotate_df,anno_d, anno_alias in [(0,ax1,to_annotate1,anno_d1,anno_alias1),(1,ax5,to_annotate5,anno_d2,anno_alias2)]:
             ###################### annotate() args
             if to_annotate_df.empty is True:
-                if verbose: log.write(" -Skipping annotation...")
+                log.write(" -Skipping annotation...", verbose=verbose)
                 continue
 
             fontweight = "normal"
@@ -313,7 +313,7 @@ def annotate_pair(
                             annotation_col=anno
                         else:
                             annotation_col=anno+"_"+str(index+1)
-                if verbose: log.write(" -Annotating using column "+annotation_col+"...")
+                log.write(" -Annotating using column "+annotation_col+"...", verbose=verbose)
                 
                 ## calculate y span
                 if region is not None:
@@ -453,7 +453,7 @@ def annotate_pair(
                     anno_count +=1
             
             if anno_adjust==True:
-                if verbose: log.write(" -Auto-adjusting text positions for plot {}...".format(index))
+                log.write(" -Auto-adjusting text positions for plot {}...".format(index), verbose=verbose)
                 if index==0:
                     va="bottom"
                     ha='left'
@@ -476,7 +476,7 @@ def annotate_pair(
                             lim =anno_max_iter
                             )
     else:
-        if verbose: log.write(" -Skip annotating")
+        log.write(" -Skip annotating", verbose=verbose)
     return ax1,ax5
 
 
@@ -521,7 +521,7 @@ def annotate_subtype(
                 annotation_col="CHR:POS"
         elif anno:
                 annotation_col=anno
-        if verbose: log.write(" -Annotating using column "+annotation_col+"...")
+        log.write(" -Annotating using column "+annotation_col+"...", verbose=verbose)
         
         ## calculate y span
         if region is not None:
@@ -529,7 +529,7 @@ def annotate_subtype(
         else:
             y_span = sumstats["i"].max()-sumstats["i"].min()
         
-        if verbose: log.write(" -Adjusting text positions with repel_force={}...".format(repel_force))
+        log.write(" -Adjusting text positions with repel_force={}...".format(repel_force), verbose=verbose)
         if anno_style == "expand" :
             to_annotate.loc[:, "ADJUSTED_i"] = adjust_text_position(to_annotate["i"].values.copy(), y_span, repel_force,max_iter=anno_max_iter,log=log,verbose=verbose)
         ##  iterate through variants to be annotated
@@ -656,7 +656,7 @@ def annotate_subtype(
             anno_count +=1
         #anno_adjust_keyargs = {"arrowprops":dict(arrowstyle='->', color='grey', linewidth=0.1,relpos=(0.5,0.5))}
         if anno_adjust==True:
-            if verbose: log.write(" -Auto-adjusting text positions...")
+            log.write(" -Auto-adjusting text positions...", verbose=verbose)
             adjust_text(texts = anno_to_adjust_list,
                         autoalign=False, 
                         only_move={'points':'x', 'text':'x', 'objects':'x'},
@@ -674,7 +674,7 @@ def annotate_subtype(
                         )
         
     else:
-        if verbose: log.write(" -Skip annotating")
+        log.write(" -Skip annotating", verbose=verbose)
     
     return ax1
 

gwaslab/viz_aux_quickfix.py

@@ -5,7 +5,7 @@ from gwaslab.bd_common_data import get_chr_to_number
 from gwaslab.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",verbose=True, log=Log()):
+def _quick_fix(sumstats, chr_dict=get_chr_to_number(), scaled=False, chrom="CHR", pos="POS", p="P", mlog10p="MLOG10P",log=Log(), verbose=True):
     '''
     quick sanity check for input sumstats
     '''
@@ -31,39 +31,40 @@ def _quick_fix_p_value(sumstats, p="P", mlog10p="MLOG10P", scaled=False,verbose=
     '''
     if scaled==True:
         # if scaled, add scaled P and P col 
-        if verbose:log.write(" -P values are already scaled...")
-        if verbose:log.write(" -Sumstats -log10(P) values are being converted to P...")
+        log.write(" -P values are already scaled...", verbose=verbose)
+        log.write(" -Sumstats -log10(P) values are being converted to P...", verbose=verbose)
         sumstats["scaled_P"] = sumstats[mlog10p].copy()
         sumstats[p]= np.power(10,-sumstats[mlog10p].astype("float64"))
         return sumstats
     # bad p : na and outside (0,1]
     bad_p_value = (sumstats[p].isna()) | (sumstats[p] > 1) | (sumstats[p] <= 0)
-    if verbose:
-        log.write(" -Sanity check after conversion: " + str(sum(bad_p_value)) +
-                  " variants with P value outside of (0,1] will be removed...")
+
+    log.write(" -Sanity check after conversion: " + str(sum(bad_p_value)) +
+                  " variants with P value outside of (0,1] will be removed...", verbose=verbose)
     sumstats = sumstats.loc[~bad_p_value, :]
     return sumstats
 
 
-def _quick_fix_mlog10p(sumstats,p="P", mlog10p="MLOG10P", scaled=False, verbose=True, log=Log()):
+def _quick_fix_mlog10p(insumstats,p="P", mlog10p="MLOG10P", scaled=False, log=Log(), verbose=True):
     '''
     drop variants with bad -log10(P) values
     '''
+    sumstats = insumstats.copy()
     if scaled != True:
-        if verbose:log.write(" -Sumstats P values are being converted to -log10(P)...")
+        log.write(" -Sumstats P values are being converted to -log10(P)...", verbose=verbose)
         sumstats["scaled_P"] = -np.log10(sumstats[p].astype("float64"))
         
     #with pd.option_context('mode.use_inf_as_na', True):
     #    is_na = sumstats["scaled_P"].isna()
     if_inf_na = np.isinf(sumstats["scaled_P"]) | sumstats["scaled_P"].isna()
-    if verbose:
-        log.write(" -Sanity check: "+str(sum(if_inf_na)) +
-                  " na/inf/-inf variants will be removed...")
+
+    log.write(" -Sanity check: "+str(sum(if_inf_na)) +
+                  " na/inf/-inf variants will be removed...", verbose=verbose)
     sumstats = sumstats.loc[~if_inf_na, :]
     return sumstats
 
 
-def _quick_fix_eaf(seires, verbose=True, log=Log()):
+def _quick_fix_eaf(seires,log=Log(), verbose=True):
     '''
     conversion of eaf to maf
     '''
@@ -73,7 +74,7 @@ def _quick_fix_eaf(seires, verbose=True, log=Log()):
     return seires.copy()
 
 
-def _quick_fix_chr(seires, chr_dict, verbose=True, log=Log()):
+def _quick_fix_chr(seires, chr_dict,log=Log(), verbose=True):
     '''
     conversion and check for chr
     '''
@@ -84,7 +85,7 @@ def _quick_fix_chr(seires, chr_dict, verbose=True, log=Log()):
     return seires
 
 
-def _quick_fix_pos(seires, verbose=True, log=Log()):
+def _quick_fix_pos(seires,log=Log(), verbose=True):
     '''
     force conversion for pos
     '''
@@ -92,7 +93,7 @@ def _quick_fix_pos(seires, verbose=True, log=Log()):
     return seires
 
 
-def _get_largenumber(*args, log=Log()):
+def _get_largenumber(*args,log=Log(), verbose=True):
     '''
     get a helper large number, >> max(pos)
     '''
@@ -104,11 +105,11 @@ def _get_largenumber(*args, log=Log()):
         else:
             break
         if i == 7:
-            log.write(" -Warning: max POS is too large!")
+            log.warning("Max POS is too large!")
     return large_number
 
 
-def _quick_add_tchrpos(sumstats, chr="chr", pos="POS", large_number=10000000000, dropchrpos=False, verbose=True, log=Log()):
+def _quick_add_tchrpos(sumstats, chr="chr", pos="POS", large_number=10000000000, dropchrpos=False,log=Log(), verbose=True):
     sumstats["TCHR+POS"] = sumstats["CHR"]*large_number + sumstats["POS"]
     sumstats["TCHR+POS"] = sumstats["TCHR+POS"].astype('Int64')
     if dropchrpos == True:
@@ -117,7 +118,7 @@ def _quick_add_tchrpos(sumstats, chr="chr", pos="POS", large_number=10000000000,
     return sumstats
 
 
-def _quick_merge_sumstats(sumstats1, sumstats2):
+def _quick_merge_sumstats(sumstats1, sumstats2, log=Log(), verbose=True):
     merged_sumstats = pd.merge(sumstats1, sumstats2, on="TCHR+POS", how="outer", suffixes=('_1', '_2'))
     merged_sumstats["CHR"] = merged_sumstats["CHR_1"]
     merged_sumstats["POS"] = merged_sumstats["POS_1"]
@@ -126,7 +127,7 @@ def _quick_merge_sumstats(sumstats1, sumstats2):
     merged_sumstats = merged_sumstats.drop(labels=["CHR_1", "CHR_2", "POS_1", "POS_2"],axis=1)
     return merged_sumstats
 
-def _quick_assign_i(sumstats, chrom="CHR",pos="POS"):
+def _quick_assign_i(sumstats, chrom="CHR",pos="POS",log=Log(), verbose=True):
     # sort by CHR an POS
     sumstats = sumstats.sort_values([chrom,pos])
     # set new id
@@ -158,7 +159,7 @@ def _quick_assign_i(sumstats, chrom="CHR",pos="POS"):
     sumstats["i"] = np.floor(pd.to_numeric(sumstats["i"], errors='coerce')).astype('Int64')
     return sumstats, chrom_df
 
-def _quick_assign_i_with_rank(sumstats, chrpad, use_rank=False, chrom="CHR",pos="POS",drop_chr_start=False,_posdiccul=None):
+def _quick_assign_i_with_rank(sumstats, chrpad, use_rank=False, chrom="CHR",pos="POS",drop_chr_start=False,_posdiccul=None,log=Log(), verbose=True):
     # align all variants on a single axis (i)
     sumstats = sumstats.sort_values([chrom,pos])
     if use_rank is True: 
@@ -218,7 +219,7 @@ def _quick_assign_i_with_rank(sumstats, chrpad, use_rank=False, chrom="CHR",pos=
     sumstats["i"] = np.floor(pd.to_numeric(sumstats["i"], errors='coerce')).astype('Int64')
     return sumstats, chrom_df
 
-def _quick_assign_marker_relative_size(series, sig_level = 5e-8, suggestive_sig_level=5e-6, lower_level=5e-4):
+def _quick_assign_marker_relative_size(series, sig_level = 5e-8, suggestive_sig_level=5e-6, lower_level=5e-4,log=Log(), verbose=True):
     size_series = series.copy()
     size_series[:] = 1
 
@@ -231,7 +232,7 @@ def _quick_assign_marker_relative_size(series, sig_level = 5e-8, suggestive_sig_
     size_series[is_sig_level] = 4
     return size_series
 
-def _quick_assign_highlight_hue(sumstats,highlight,highlight_windowkb, snpid="SNPID",chrom="CHR",pos="POS",verbose=True, log=Log()):
+def _quick_assign_highlight_hue(sumstats,highlight,highlight_windowkb, snpid="SNPID",chrom="CHR",pos="POS",log=Log(), verbose=True):
     to_highlight = sumstats.loc[sumstats[snpid].isin(highlight),:]
     #assign colors: 0 is hightlight color
     for i,row in to_highlight.iterrows():
@@ -243,7 +244,7 @@ def _quick_assign_highlight_hue(sumstats,highlight,highlight_windowkb, snpid="SN
         sumstats.loc[right_chr&up_pos&low_pos,"HUE"]="0"
     return sumstats
 
-def _quick_assign_highlight_hue_pair(sumstats, highlight1, highlight2, highlight_windowkb, chrom="CHR",pos="POS",verbose=True, log=Log()):
+def _quick_assign_highlight_hue_pair(sumstats, highlight1, highlight2, highlight_windowkb, chrom="CHR",pos="POS",log=Log(), verbose=True):
     #assign colors: 0 is hightlight color
     to_highlight1 = pd.DataFrame()
     to_highlight2 = pd.DataFrame()
@@ -271,34 +272,35 @@ def _quick_assign_highlight_hue_pair(sumstats, highlight1, highlight2, highlight
             sumstats.loc[right_chr&up_pos&low_pos,"HUE2"]="0"
     return sumstats, to_highlight1, to_highlight2
 
-def _quick_extract_snp_in_region(sumstats, region, chrom="CHR",pos="POS",verbose=True, log=Log()):
+def _quick_extract_snp_in_region(sumstats, region, chrom="CHR",pos="POS",log=Log(), verbose=True):
     region_chr = region[0]
     region_start = region[1]
     region_end = region[2]
-    if verbose:log.write(" -Extract SNPs in region : chr"+str(region_chr)+":"+str(region[1])+"-"+str(region[2])+ "...")
+    log.write(" -Extract SNPs in region : chr"+str(region_chr)+":"+str(region[1])+"-"+str(region[2])+ "...", verbose=verbose)
     is_in_region_snp = (sumstats[chrom]==region_chr) &(sumstats[pos]<region_end) &(sumstats[pos]>region_start)
-    if verbose:log.write(" -Extract SNPs in specified regions: "+str(sum(is_in_region_snp)))
+    log.write(" -Extract SNPs in specified regions: "+str(sum(is_in_region_snp)), verbose=verbose)
     sumstats = sumstats.loc[is_in_region_snp,:]
     return sumstats
 
-def _cut(series, mode,cutfactor,cut,skip, ylabels, cut_log, verbose,lines_to_plot, log):
+def _cut(series, mode,cutfactor,cut,skip, ylabels, cut_log, verbose, lines_to_plot, log):
+    log.write(" -Converting data above cut line...",verbose=verbose)
     if ylabels is not None:
         ylabels = pd.Series(ylabels)
     maxy = series.max()
     series = series.copy()
     if "b" not in mode:
-        if verbose: log.write(" -Maximum -log10(P) value is "+str(maxy) +" .")
+        log.write(" -Maximum -log10(P) value is "+str(maxy) +" .", verbose=verbose)
     elif "b" in mode:
-        if verbose: log.write(" -Maximum DENSITY value is "+str(maxy) +" .")
+        log.write(" -Maximum DENSITY value is "+str(maxy) +" .", verbose=verbose)
     
     maxticker=int(np.round(series.max(skipna=True)))
     
     if cut:
         # auto mode : determine curline and cut factor
         if cut==True:
-            if verbose: log.write(" -Cut Auto mode is activated...")
+            log.write(" -Cut Auto mode is activated...", verbose=verbose)
             if maxy<30:
-                if verbose: log.write(" - maxy <30 , no need to cut.")
+                log.write(" - maxy <30 , no need to cut.", verbose=verbose)
                 cut=0
             else:
                 cut = 20
@@ -325,9 +327,9 @@ def _cut(series, mode,cutfactor,cut,skip, ylabels, cut_log, verbose,lines_to_plo
             else:
                 # cut linear mode
                 if "b" not in mode:
-                    if verbose: log.write(" -Minus log10(P) values above " + str(cut)+" will be shrunk with a shrinkage factor of " + str(cutfactor)+"...")
+                    log.write(" -Minus log10(P) values above " + str(cut)+" will be shrunk with a shrinkage factor of " + str(cutfactor)+"...", verbose=verbose)
                 else:
-                    if verbose: log.write(" -Minus DENSITY values above " + str(cut)+" will be shrunk with a shrinkage factor of " + str(cutfactor)+"...")
+                    log.write(" -Minus DENSITY values above " + str(cut)+" will be shrunk with a shrinkage factor of " + str(cutfactor)+"...", verbose=verbose)
 
                 maxticker=int(np.round(series.max(skipna=True)))
 
@@ -340,7 +342,7 @@ def _cut(series, mode,cutfactor,cut,skip, ylabels, cut_log, verbose,lines_to_plo
                 #sumstats.loc[sumstats["scaled_P"]>cut,"scaled_P"] = (sumstats.loc[sumstats["scaled_P"]>cut,"scaled_P"]-cut)/cutfactor +  cut
                 
                 maxy = (maxticker-cut)/cutfactor + cut
-    if verbose: log.write("Finished data conversion and sanity check.")
+    
     return series, maxy, maxticker, cut, cutfactor,ylabels,lines_to_plot
 
 #def _cut_line(level, mode,cutfactor,cut,skip, ylabels, cut_log, verbose, log):
@@ -362,9 +364,11 @@ def _set_yticklabels(cut,
                      font_family,
                      ytick3,
                      ylabels,
-                     ylabels_converted
+                     ylabels_converted,
+                     log=Log(),
+                     verbose=True
                      ):
-    
+    log.write(" -Processing Y tick lables...",verbose=verbose)
     # if no cut
     if cut == 0: 
             ax1.set_ylim(skip, ceil(maxy*1.2) )
@@ -430,7 +434,8 @@ def _set_yticklabels(cut,
     
     return ax1
 
-def _jagged_y(cut,skip,ax1,mode,mqqratio,jagged_len,jagged_wid):
+def _jagged_y(cut,skip,ax1,mode,mqqratio,jagged_len,jagged_wid, log=Log(), verbose=True):
+    log.write(" -Processing jagged Y axis...",verbose=verbose)
     tycut = cut +0.3 #(cut - skip)/ (ax1.get_ylim()[1] - skip) + 0.002
     dy= jagged_len * (cut - skip) 
     x0 =  0

gwaslab/viz_aux_reposition_text.py

@@ -2,23 +2,25 @@ import pandas as pd
 import numpy as np
 from gwaslab.g_Log import Log
 
-def adjust_text_position(positions, yspan, repel_force=0.01, max_iter=100,amode="int",log=Log(),verbose=True):
+def adjust_text_position(positions, yspan, repel_force=0.01, max_iter=100,amode="int",log=Log(),verbose=True, min_factor=None):
     # check the number of variants to annotate 
     #if repel_force>0:
     #    if 1/(repel_force*2 +0.01) < len(positions):
-    #        if verbose: log.write(" -Too many variants to annotate; maybe it is better to reduce the number of variants")
+    #        log.write(" -Too many variants to annotate; maybe it is better to reduce the number of variants")
     #else:
     if len(positions)>30:
-        if verbose: log.write(" -Too many variants to annotate; maybe it is better to reduce the number of variants")
+        log.write(" -Too many variants to annotate; maybe it is better to reduce the number of variants",verbose=verbose)
 
     # calculate the steps
     if amode=="int":
         step = int(yspan*repel_force) 
     elif amode=="log":
-        min_factor = np.min(positions)
+        if min_factor is None:
+            min_factor = np.min(positions)
         #(1, max) -> (0, log(max)))
-        positions = np.log(positions/min_factor)
+        positions = np.log2(positions/min_factor)
         step = max(positions)*repel_force 
+
     else:
         step = yspan*repel_force 
 
@@ -33,7 +35,8 @@ def adjust_text_position(positions, yspan, repel_force=0.01, max_iter=100,amode=
             if amode=="int":
                 return  np.floor(pd.to_numeric(positions, errors='coerce')).astype('Int64').copy()
             elif amode=="log":
-                return  np.exp(pd.to_numeric(positions, errors='coerce')) * min_factor
+                
+                return  np.power(2, pd.to_numeric(positions, errors='coerce'))* min_factor
             else:
                 return  pd.to_numeric(positions, errors='coerce')
         else:
@@ -44,7 +47,7 @@ def adjust_text_position(positions, yspan, repel_force=0.01, max_iter=100,amode=
                 move_position_from_center_float(positions, index, step)
     
     # when reaching maximum iteration, return anyway
-    if verbose: log.write(" -Reaching maximum iteration: {}; Skipping...".format(max_iter))
+    log.write(" -Reaching maximum iteration: {}; Skipping...".format(max_iter),verbose=verbose)
     if amode=="int":
         return np.floor(pd.to_numeric(positions, errors='coerce')).astype('Int64').copy()
     elif amode=="log":

gwaslab/viz_aux_save_figure.py

@@ -4,23 +4,33 @@ import time
 import os.path
 
 def save_figure(fig, save, keyword, save_args=None, log = Log(), verbose=True):
+    log.write("Start to save figure..." ,verbose=verbose)
     if save_args is None:
         save_args = {}
+        
     if save:
-        if verbose: log.write("Saving plot:")
         if save==True:
             default_path = get_default_path(keyword)
             fig.savefig(default_path, bbox_inches="tight",**save_args)
-            log.write(" -Saved to "+ default_path + " successfully!" )
+            log.write(" -Saved to "+ default_path + " successfully!" ,verbose=verbose)
         else:
-            if os.path.exists(save):
-                fig.savefig(save,bbox_inches="tight",**save_args)
-                log.write(" -Saved to "+ save + " successfully! (overwrite)" )
+            if save[-3:]=="pdf":
+                if os.path.exists(save):
+                    fig.savefig(save, **save_args)
+                    log.write(" -Saved to "+ save + " successfully! (pdf, overwrite)" ,verbose=verbose)
+                else:
+                    fig.savefig(save, **save_args)
+                    log.write(" -Saved to "+ save + " successfully! (pdf)" ,verbose=verbose)
             else:
-                fig.savefig(save,bbox_inches="tight",**save_args)
-                log.write(" -Saved to "+ save + " successfully!" )
+                if os.path.exists(save):
+                    fig.savefig(save,bbox_inches="tight",**save_args)
+                    log.write(" -Saved to "+ save + " successfully! (overwrite)" ,verbose=verbose)
+                else:
+                    fig.savefig(save,bbox_inches="tight",**save_args)
+                    log.write(" -Saved to "+ save + " successfully!" ,verbose=verbose)
     else:
-        log.write(" -Skip saving figures!" )
+        log.write(" -Skip saving figure!" ,verbose=verbose)
+    log.write("Finished saving figure..." ,verbose=verbose)
 
 def get_default_path(keyword,fmt="png"):
     path_dictionary = { 

gwaslab/viz_plot_compare_af.py

@@ -10,6 +10,7 @@ from gwaslab.viz_aux_save_figure import save_figure
 def plotdaf(sumstats,
              eaf="EAF",
              daf="DAF",
+             raf="RAF",
              threshold=0.16,
              xlabel="Alternative Allele Frequency in Reference Population (RAF)",
              ylabel="Effect Allele Frequency in Sumstats (EAF)",
@@ -43,7 +44,7 @@ def plotdaf(sumstats,
     if plt_args is None:
         plt_args={"figsize":(8,4),"dpi":300}
     if histplot_args is None:
-        histplot_args={"log_scale":(False,True)}
+        histplot_args={"log_scale":(False,False)}
     if reg_line_args is None:
         reg_line_args={"color":'#cccccc', "linestyle":'--'}
     if threshold_line_args is None:
@@ -55,8 +56,9 @@ def plotdaf(sumstats,
     if save_args is None:
         save_args =  {}
 
-    if verbose: log.write("Start to plot Reference frequency vs Effect allele frequency plot...")
-    if not ((eaf in sumstats.columns) and (daf in sumstats.columns)):
+    log.write("Start to plot allele frequency comparison plot...", verbose=verbose)
+    
+    if not ((eaf in sumstats.columns) and ((daf in sumstats.columns)) or (raf in sumstats.columns)):
         raise ValueError("EAF and/or DAF columns were not detected.")
     
     if "SNPID" in sumstats.columns:
@@ -70,40 +72,42 @@ def plotdaf(sumstats,
     if "NEA" in sumstats.columns:
         alleles.append("NEA")
     
+    if daf not in sumstats.columns:
+        sumstats[daf] = sumstats[eaf] - sumstats[raf]
 
     sumstats = sumstats.loc[(~sumstats[eaf].isna())&(~sumstats[daf].isna()),[snpid,eaf,daf]+alleles].copy()
-    sumstats.loc[:,daf] = sumstats.loc[:,daf].astype("float")
-    sumstats.loc[:,eaf] = sumstats.loc[:,eaf].astype("float")
-    if verbose: log.write(" -Plotting valriants:" + str(len(sumstats)))
-    
-    sumstats.loc[:,"RAF"]=sumstats[eaf] - sumstats[daf]
+    sumstats[daf] = sumstats[daf].astype("float")
+    sumstats[eaf] = sumstats[eaf].astype("float")
+    log.write(" -Plotting valriants:" + str(len(sumstats)), verbose=verbose)
+    if raf not in sumstats.columns:
+        sumstats[raf] = sumstats[eaf] - sumstats[daf]
     sns.set_style("ticks")
-    fig, (ax1, ax2) = plt.subplots(1, 2,**plt_args)
-    ax1.scatter(sumstats["RAF"],sumstats[eaf],label="Non-outlier", **scatter_args)
+    fig, [ax1, ax2] = plt.subplots(1, 2,**plt_args)
+    ax1.scatter(sumstats[raf],sumstats[eaf],label="Non-outlier", **scatter_args)
     
     if is_threshold is True:
         is_outliers = sumstats[daf].abs() > threshold 
         if sum(is_outliers)>0:
-            ax1.scatter(sumstats.loc[is_outliers, "RAF"],sumstats.loc[is_outliers, eaf],label="Outlier", **scatter_args_outlier)
+            ax1.scatter(sumstats.loc[is_outliers, raf],sumstats.loc[is_outliers, eaf],label="Outlier", **scatter_args_outlier)
     
     if legend1 ==True:
         ax1.legend()
     
     if is_reg is True:
-        if verbose: log.write(" -Plotting regression line...")
-        reg = ss.linregress(sumstats["RAF"],sumstats[eaf])
-        if verbose:log.write(" -Beta = ", reg[0])
-        if verbose:log.write(" -Intercept = ", reg[1])
-        if verbose:log.write(" -R2 = ", reg[2])
+        log.write(" -Plotting regression line...", verbose=verbose)
+        reg = ss.linregress(sumstats[raf],sumstats[eaf])
+        log.write(" -Beta = ", reg[0], verbose=verbose)
+        log.write(" -Intercept = ", reg[1], verbose=verbose)
+        log.write(" -R2 = ", reg[2], verbose=verbose)
         ax1.axline(xy1=(0,reg[1]),slope=reg[0],zorder=1,**reg_line_args)
         if r2 is True:
             ax1.text(0.98,0.02, "$R^2 = {:.3f}$".format(reg[2]), transform=ax1.transAxes, **r2_args)
 
     if is_threshold is True:
-        if verbose: log.write(" -Threshold : " + str(threshold))
+        log.write(" -Threshold : " + str(threshold), verbose=verbose)
         num = sum(np.abs(sumstats[daf])>threshold )
-        if verbose: log.write(" -Variants with relatively large DAF : ",num )
-        if verbose: log.write(" -Percentage for variants with relatively large DAF : ",num/len(sumstats) )
+        log.write(" -Variants with relatively large DAF : ",num , verbose=verbose)
+        log.write(" -Percentage for variants with relatively large DAF : ",num/len(sumstats) , verbose=verbose)
         ax1.axline(xy1=(0,threshold),slope=1,zorder=1,**threshold_line_args)
         ax1.axline(xy1=(threshold,0),slope=1,zorder=1,**threshold_line_args)
     
@@ -119,25 +123,20 @@ def plotdaf(sumstats,
     ax1.set_ylim([0,1])
     
 
-    sumstats.loc[:,"ID"] = sumstats.index
+    sumstats["ID"] = sumstats.index
     
-    to_plot = pd.melt(sumstats,id_vars=['ID'], value_vars=['EAF',"RAF"], var_name='Types', value_name='Allele Frequency')
-    
-    sns.histplot(data=to_plot, x="Allele Frequency", hue="Types", fill=True, ax=ax2, legend = legend2 ,**histplot_args)
-    ax2.set_xlabel("Allele Frequency",**font_args)
+    to_plot = pd.melt(sumstats,id_vars=['ID'], value_vars=[eaf,raf], var_name='Types', value_name='Allele Frequency').dropna()
 
+    sns.histplot(data=to_plot, x="Allele Frequency", 
+                 hue="Types", fill=True, 
+                 ax=ax2, legend = legend2,
+                 **histplot_args)
+ 
+    ax2.set_xlabel("Allele Frequency",**font_args)
 
     plt.tight_layout()
     save_figure(fig, save, keyword="afc",save_args=save_args, log=log, verbose=verbose)
-
-    #if save:
-    #    if verbose: log.write("Saving plot:")
-    #    if save==True:
-    #        fig.savefig("./allele_frequency_comparison.png",bbox_inches="tight",**save_args)
-    #        log.write(" -Saved to "+ "./allele_frequency_comparison.png" + " successfully!" )
-    #    else:
-    #        fig.savefig(save,bbox_inches="tight",**save_args)
-    #        log.write(" -Saved to "+ save + " successfully!" )
     sumstats = sumstats.drop(columns="ID")
+
     return fig, sumstats[is_outliers].copy()