gwaslab 3.5.1__tar.gz → 3.5.2__tar.gz

{gwaslab-3.5.1/src/gwaslab.egg-info → gwaslab-3.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.5.1
+Version: 3.5.2
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/

{gwaslab-3.5.1 → gwaslab-3.5.2}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gwaslab"
-version = "3.5.1"
+version = "3.5.2"
 authors = [
   { name="Yunye", email="yunye@gwaslab.com" },
 ]

{gwaslab-3.5.1 → gwaslab-3.5.2}/src/gwaslab/__init__.py

@@ -46,3 +46,4 @@ from gwaslab.util_ex_process_h5 import process_vcf_to_hfd5
 from gwaslab.util_ex_run_susie import _run_susie_rss as run_susie_rss
 from gwaslab.io_read_tabular import _read_tabular as read_tabular
 from gwaslab.util_in_meta import meta_analyze
+from gwaslab.viz_plot_scatter_with_reg import scatter

{gwaslab-3.5.1 → gwaslab-3.5.2}/src/gwaslab/g_Sumstats.py

@@ -389,6 +389,12 @@ class Sumstats():
             self.data =flipallelestats(self.data,log=self.log,**flipallelestats_args)
             
             gc.collect()
+            
+        if (ref_seq is not None or ref_infer is not None) and (ref_rsid_tsv is not None or ref_rsid_vcf is not None):
+
+            self.data = fixID(self.data, log=self.log, **{"fixid":True, "fixsep":True, "overwrite":True})
+
+            gc.collect()
         
         #####################################################
         if ref_rsid_tsv is not None:
@@ -833,4 +839,4 @@ class Sumstats():
     def to_format(self, path, build=None, verbose=True, **kwargs):
         if build is None:
             build = self.meta["gwaslab"]["genome_build"]
-        _to_format(self.data, path, log=self.log, verbose=verbose, meta=self.meta, build=build, **kwargs)
+        _to_format(self.data, path, log=self.log, verbose=verbose, meta=self.meta, build=build, **kwargs)

{gwaslab-3.5.1 → gwaslab-3.5.2}/src/gwaslab/g_version.py

@@ -15,8 +15,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.5.1",
-   "release_date":"20241120"
+   "version":"3.5.2",
+   "release_date":"20241203"
     }
     return dic   
 

{gwaslab-3.5.1 → gwaslab-3.5.2}/src/gwaslab/io_process_args.py

@@ -1,15 +1,13 @@
 import copy
-def _merge_and_sync_dic(list_of_dics:list, default:dict) -> dict:
-    temp = copy.copy(default)
-    for dic in list_of_dics:
-        if isinstance(dic, dict):
-            temp.update(dic)
-    return temp
 
 def _list_func_args(func):
     return func.__code__.co_varnames
 
 def _extract_kwargs(prefix:str, default:dict, kwargs:dict) -> dict:
+    # prefix: keyword
+    # default: default dict
+    # kwargs: all local kwargs  + args + kwargs
+
     extracted = []
     for key,value in kwargs.items():
         if key=="kwargs" or key=="args":
@@ -20,4 +18,11 @@ def _extract_kwargs(prefix:str, default:dict, kwargs:dict) -> dict:
             if prefix in key and "arg" in key:
                 extracted.append(value)
     merged_arg = _merge_and_sync_dic(extracted, default)
-    return merged_arg
+    return merged_arg
+
+def _merge_and_sync_dic(list_of_dics:list, default:dict) -> dict:
+    temp = copy.copy(default)
+    for dic in list_of_dics:
+        if isinstance(dic, dict):
+            temp.update(dic)
+    return temp

{gwaslab-3.5.1 → gwaslab-3.5.2}/src/gwaslab/viz_aux_quickfix.py

@@ -1,6 +1,8 @@
 import pandas as pd
 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 math import ceil
@@ -350,7 +352,7 @@ def _cut(series, mode,cutfactor,cut,skip, ylabels, cut_log, verbose, lines_to_pl
                 #sumstats.loc[sumstats["scaled_P"]>cut,"scaled_P"] = (sumstats.loc[sumstats["scaled_P"]>cut,"scaled_P"]-cut)/cutfactor +  cut
                 
                 maxy = (maxticker-cut)/cutfactor + cut
-    
+
     return series, maxy, maxticker, cut, cutfactor,ylabels,lines_to_plot
 
 #def _cut_line(level, mode,cutfactor,cut,skip, ylabels, cut_log, verbose, log):
@@ -379,10 +381,9 @@ def _set_yticklabels(cut,
     log.write(" -Processing Y tick lables...",verbose=verbose)
     # if no cut
     if cut == 0: 
-            ax1.set_ylim(skip, ceil(maxy*1.2) )
-
+            ax1.set_ylim((skip, ceil(maxy*1.2)) )
     # if cut     
-    if cut:
+    if cut!=0:
         # add cut line
         
         cutline = ax1.axhline(y=cut, linewidth = sc_linewidth,linestyle="--",color=cut_line_color,zorder=1)
@@ -432,14 +433,15 @@ def _set_yticklabels(cut,
         else:
             ax1.set_yticks(ticks1+ticks2)
             ax1.set_yticklabels(tickslabel1+tickslabel2,fontsize=fontsize,family=font_family)
-        ax1.set_ylim(bottom = skip)
     
     if ylabels is not None:  
         ax1.set_yticks(ylabels_converted)
         ax1.set_yticklabels(ylabels,fontsize=fontsize,family=font_family)
     
+    ylim_top = ax1.get_ylim()[1]
+    ax1.set_ybound(lower=skip,upper=ylim_top)
     ax1.tick_params(axis='y', labelsize=fontsize)
-    
+
     return ax1
 
 def _jagged_y(cut,skip,ax1,mode,mqqratio,jagged_len,jagged_wid, log=Log(), verbose=True):

{gwaslab-3.5.1 → gwaslab-3.5.2}/src/gwaslab/viz_aux_save_figure.py

@@ -51,7 +51,8 @@ def get_default_path(keyword,fmt="png"):
                         "miami":"miami",
                         "esc":"effect_size_comparision",
                         "afc":"allele_frequency_comparision",
-                        "gwheatmap":"genome_wide_heatmap"
+                        "gwheatmap":"genome_wide_heatmap",
+                        "scatter":"scatter"
                         }
     prefix = path_dictionary[keyword]
     count = 1

{gwaslab-3.5.1 → gwaslab-3.5.2}/src/gwaslab/viz_plot_mqqplot.py

@@ -264,7 +264,7 @@ def mqqplot(insumstats,
         
     if region_marker_shapes is None:
         # 9 shapes
-        region_marker_shapes = ['o', 's','^','D','*','P','X','h','8']
+        region_marker_shapes = ['o', '^','s','D','*','P','X','h','8']
     if region_grid_line is None:
         region_grid_line = {"linewidth": 2,"linestyle":"--"}
     if region_lead_grid_line is None:
@@ -640,6 +640,14 @@ def mqqplot(insumstats,
             linewidth=1
             if len(region_ref) == 1:
                 palette = {100+i:region_ld_colors[i] for i in range(len(region_ld_colors))}
+                scatter_args["markers"]= {(i+1):m for i,m in enumerate(region_marker_shapes[:2])}
+                if region_ref[0] is None:
+                    id_to_hide = sumstats["scaled_P"].idxmax()
+                    sumstats.loc[id_to_hide,"s"] = -100
+                else:
+                    sumstats.loc[sumstats["SNPID"]==region_ref[0],"s"] = -100
+                marker_size=(0,marker_size[1])
+                style="SHAPE"
             else:
                 palette = {}
                 region_color_maps = []
@@ -652,12 +660,14 @@ def mqqplot(insumstats,
                         # 1 + 5 + 1
                         region_ld_colors_single = [region_ld_colors[0]] + output_hex_colors + [output_hex_colors[-1]]
                     region_color_maps.append(region_ld_colors_single)
-                # gradient colors
+                
+                # gradient color dict
                 for i, hex_colors in enumerate(region_color_maps):
                     for j, hex_color in enumerate(hex_colors):
                         palette[(i+1)*100 + j ] = hex_color
 
                 edgecolor="none"
+                # create a marker shape dict
                 scatter_args["markers"]= {(i+1):m for i,m in enumerate(region_marker_shapes[:len(region_ref)])}
                 style="SHAPE"
 
@@ -1396,14 +1406,19 @@ def _process_xtick(ax1, chrom_df, xtick_chr_dict, fontsize, font_family, log=Log
 
 def _process_ytick(ax1, fontsize, font_family, ax4, log=Log(),verbose=True):
     log.write(" -Processing Y labels...",verbose=verbose)
-    ax1_yticklabels = ax1.get_yticklabels()
+    #ax1_yticklabels = ax1.get_yticklabels()
+    #print(ax1_yticklabels)
+    #plt.draw()
+    #ax1_yticks = ax1.get_yticks()
+    #print(ax1_yticks)
     #ax1.set_yticklabels(ax1_yticklabels,fontsize=fontsize,family=font_family) 
-    ax1_yticks = ax1.get_yticks()
-    ax1.set_yticks(ax1_yticks,ax1_yticklabels,fontsize=fontsize,family=font_family) 
+    ax1.tick_params(axis='y', labelsize=fontsize,labelfontfamily=font_family)
+    #ax1.set_yticks(ax1_yticks,ax1_yticklabels,fontsize=fontsize,family=font_family) 
     if ax4 is not None:
-        ax4_yticklabels = ax4.get_yticklabels()
-        ax4_yticks = ax4.get_yticks()
-        ax4.set_yticks(ax4_yticks,ax4_yticklabels, fontsize=fontsize,family=font_family) 
+        #ax4_yticklabels = ax4.get_yticklabels()
+        #ax4_yticks = ax4.get_yticks()
+        ax4.tick_params(axis='y', labelsize=fontsize,labelfontfamily=font_family)
+        #ax4.set_yticks(ax4_yticks,ax4_yticklabels, fontsize=fontsize,family=font_family) 
     return ax1, ax4
 
 def _process_xlabel(region, xlabel, ax1, gtf_path, mode, fontsize, font_family,  ax3=None , log=Log(),verbose=True):

{gwaslab-3.5.1 → gwaslab-3.5.2}/src/gwaslab/viz_plot_regional2.py

@@ -93,6 +93,7 @@ def _plot_regional(
             ax1, lead_id_single = _pinpoint_lead(sumstats = sumstats,
                                         ax1 = ax1, 
                                         region_ref=region_ref_single,
+                                        region_ref_total_n = len(region_ref), 
                                         lead_color = palette[(index+1)*100 + len(region_ld_threshold)+2], 
                                         marker_size= marker_size,
                                         region_marker_shapes=region_marker_shapes,
@@ -130,7 +131,9 @@ def _plot_regional(
                             region_ref=region_ref,
                             region_ld_threshold=region_ld_threshold, 
                             region_ref_index_dic=region_ref_index_dic,
-                            palette=palette)
+                            region_marker_shapes=region_marker_shapes,
+                            palette=palette,
+                            fig=fig)
         else:
             cbar=None
 
@@ -300,7 +303,7 @@ def _get_lead_id(sumstats=None, region_ref=None, log=None, verbose=True):
 
     return lead_id
 
-def _pinpoint_lead(sumstats,ax1,region_ref, lead_color, marker_size, log, verbose, region_marker_shapes):
+def _pinpoint_lead(sumstats,ax1,region_ref, region_ref_total_n, lead_color, marker_size, log, verbose, region_marker_shapes):
     
     if region_ref is None:
         log.write(" -Extracting lead variant..." , verbose=verbose)
@@ -308,12 +311,19 @@ def _pinpoint_lead(sumstats,ax1,region_ref, lead_color, marker_size, log, verbos
     else:
         lead_id = _get_lead_id(sumstats, region_ref, log, verbose)
     
+    if region_ref_total_n <2:
+        # single-ref mode
+        marker_shape = region_marker_shapes[sumstats.loc[lead_id,"SHAPE"]]
+    else:
+        # multi-ref mode
+        marker_shape = region_marker_shapes[sumstats.loc[lead_id,"SHAPE"]-1]
+
     if lead_id is not None:
         ax1.scatter(sumstats.loc[lead_id,"i"],sumstats.loc[lead_id,"scaled_P"],
                 color=lead_color,
                 zorder=3,
-                marker= region_marker_shapes[sumstats.loc[lead_id,"SHAPE"]-1],
-                s=marker_size[1]+2,
+                marker= marker_shape,
+                s=marker_size[1]*1.5,
                 edgecolor="black")
 
     return ax1, lead_id
@@ -322,14 +332,15 @@ def _add_region_title(region_title, ax1,region_title_args):
     ax1.text(0.015,0.97, region_title, transform=ax1.transAxes, va="top", ha="left", region_ref=None, **region_title_args )
     return ax1
 
-def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ref,region_ref_index_dic,palette =None, position=1):
+def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ref,region_ref_index_dic,region_marker_shapes,fig, palette =None, position=1):
     
     width_pct = "11%"
     height_pct = "{}%".format( 14 + 7 * len(region_ref))
     axins1 = inset_axes(ax1,
             width=width_pct,  # width = 50% of parent_bbox width
             height=height_pct,  # height : 5%
-            loc='upper right',axes_kwargs={"frameon":True,"facecolor":"white","zorder":999999})
+            loc='upper right',
+            axes_kwargs={"frameon":True,"facecolor":"white","zorder":999999})
     
     ld_ticks = [0]+region_ld_threshold+[1]
 
@@ -345,7 +356,7 @@ def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ref,region_ref_ind
                 a = Rectangle((x,y),width, height, fill = True, color = hex_color , linewidth = 2)
                 #patches.append(a)
                 axins1.add_patch(a)
-
+    
     # y snpid
     yticks_position = 0.1 + 0.2 *np.arange(0,len(region_ref))
     axins1.set_yticks(yticks_position, ["{}".format(x) for x in region_ref])
@@ -354,9 +365,31 @@ def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ref,region_ref_ind
     # x ld thresholds
     axins1.set_xticks(ticks=ld_ticks) 
     axins1.set_xticklabels([str(i) for i in ld_ticks]) 
-    axins1.set_xlim(0,1)    
 
+    xmin, xmax = 0, 1
+    axins1.set_xlim(xmin,xmax)    
+
+    ############### ##############plot marker ############## ##############
+    for group_index, ref in enumerate(region_ref):
+        x= -0.1
+        y= 0.1 + 0.2 * group_index
+        
+        if len(region_ref) <2:
+            # single-ref mode
+            marker = region_marker_shapes[group_index+1]
+        else:
+            # multi-ref mode
+            marker = region_marker_shapes[group_index]
+        
+        # ([x0,y0][x1,y1])
+        data_to_point =(axins1.bbox.get_points()[1][0]-axins1.bbox.get_points()[0][0]) / (xmax - xmin)
+        s =  data_to_point * 0.075
+        c =  palette[(region_ref_index_dic[region_ref[group_index]]+1)*100 + len(ld_ticks)-1]
+        axins1.scatter(x, y, s=s, marker=marker,c=c, edgecolors="black", linewidths = 1,  clip_on=False, zorder=100)
+    
+    axins1.set_xlim(0,1)   
     axins1.set_aspect('equal', adjustable='box')
+    axins1.tick_params(axis="y", pad=np.sqrt(data_to_point * 0.11))
     axins1.set_title('LD $r^{2}$ with variant',loc="center",y=-0.2)
     cbar = axins1
     return ax1, cbar
@@ -664,6 +697,9 @@ def process_vcf(sumstats,
     sumstats[final_shape_col] = 1
     sumstats[final_rsq_col] = 0.0
     
+    if len(region_ref)==1:
+        sumstats.loc[lead_id, final_shape_col] +=1 
+
     for i in range(len(region_ref)):
         ld_single = "LD_{}".format(i)
         current_rsq = "RSQ_{}".format(i)
@@ -672,7 +708,6 @@ def process_vcf(sumstats,
         sumstats.loc[a_ngt_b, final_ld_col] = 100 * (i+1) + sumstats.loc[a_ngt_b, ld_single]
         sumstats.loc[a_ngt_b, final_rsq_col] = sumstats.loc[a_ngt_b, current_rsq]
         sumstats.loc[a_ngt_b, final_shape_col] = i + 1
-
     ####################################################################################################
     log.write("Finished loading reference genotype successfully!", verbose=verbose)
     return sumstats

gwaslab-3.5.2/src/gwaslab/viz_plot_scatter_with_reg.py

@@ -0,0 +1,229 @@
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+import scipy.stats as ss
+import seaborn as sns
+import gc
+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
+
+def scatter(df, 
+            x, 
+            y,
+            mode="0",
+            reg_box=None,
+            is_reg=True,
+            fdr=False,
+            allele_match=False,
+            r_se=False,
+            is_45_helper_line=False,
+            plt_args=None,
+            xylabel_prefix="Per-allele effect size in ",
+            helper_line_args=None,
+            font_args=None,
+            fontargs=None,
+            build="19",
+            r_or_r2="r",
+            err_kwargs=None,
+            legend_args=None,
+            log = Log(),
+            save=False,
+            reg_xmin=None,
+            verbose=True,
+            save_args=None,
+            scatter_kwargs=None,
+            font_kwargs=None,
+            plt_kwargs=None,
+            null_beta=0,
+            engine="plt",
+            **kwargs):
+    
+    if save_args is None:
+        save_args = {"dpi":300,"facecolor":"white"}
+    if reg_box is None:
+        reg_box = dict(boxstyle='round', facecolor='white', alpha=1,edgecolor="None")
+    if err_kwargs is None:
+        err_kwargs={"ecolor":"#cccccc","elinewidth":1}
+    if font_kwargs is None:
+        font_kwargs={'fontsize':12,'family':'sans','fontname':'Arial'}
+    if helper_line_args is None:
+        helper_line_args={"color":'black', "linestyle":'-',"lw":1}
+    if plt_kwargs is None:
+        plt_kwargs={"figsize":(8,8),"dpi":300}
+    if scatter_kwargs is None:
+        scatter_kwargs={"s":20}
+    if reg_xmin is None:
+        reg_xmin = df[x].min()
+    
+    save_kwargs =      _extract_kwargs("save", save_args, locals())
+    err_kwargs =       _extract_kwargs("err", err_kwargs, locals())
+    plt_kwargs =       _extract_kwargs("plt", plt_kwargs,  locals())
+    scatter_kwargs =   _extract_kwargs("scatter", scatter_kwargs, locals())
+    font_kwargs =      _extract_kwargs("font",font_kwargs, locals())
+
+    log.write("Start to create scatter plot...", verbose=verbose)
+    fig,ax = plt.subplots(**plt_kwargs) 
+
+   # plot x=0,y=0, and a 45 degree line
+    xl,xh=ax.get_xlim()
+    yl,yh=ax.get_ylim()
+
+    #ax.axhline(y=0, zorder=1,**helper_line_args)
+    #ax.axvline(x=0, zorder=1,**helper_line_args)
+    
+    #for spine in ['top', 'right']:
+    #    ax.spines[spine].set_visible(False)
+    
+    log.write(" -Creating scatter plot : {} - {}...".format(x, y), verbose=verbose)
+    if engine=="plt":
+        ax.scatter(df[x],df[y],**scatter_kwargs)
+    elif engine=="sns":
+        sns.scatterplot(data=df,x=x,y=y,ax=ax,**scatter_kwargs)
+    ###regression line##############################################################################################################################
+    ax, reg = confire_regression_line(x, y,
+                                 is_reg,
+                                 reg_box, 
+                                 df, 
+                                 ax, 
+                                 mode,
+                                 xl,
+                                 yl,
+                                 xh,
+                                 yh, 
+                                 null_beta, 
+                                 r_se, 
+                                is_45_helper_line,
+                                helper_line_args, 
+                                font_kwargs,
+                                log, 
+                                verbose, reg_xmin)
+    
+    save_figure(fig = fig, save = save, keyword="scatter", save_args=save_args, log = log, verbose=verbose)
+
+    return fig, ax, reg
+
+
+def confire_regression_line(x, y, is_reg, reg_box, df,  ax, mode,xl,yl,xh,yh, null_beta, r_se, 
+                            is_45_helper_line,helper_line_args, font_kwargs,
+                            log, verbose, reg_xmin):
+    # if N <3
+    if len(df)<3: 
+        is_reg=False
+    
+    if is_reg is True:
+        # reg 
+        # slope, intercept, r, p, slope_se, intercept_se
+        if mode=="0":
+            reg = ss.linregress(df[x],df[y])
+            # estimate se for r
+            if r_se==True:
+                log.write(" -Estimating SE for rsq using Jackknife method.", verbose=verbose)
+                r_se_jackknife = jackknife_r(df,x,y,log,verbose)
+                r_se_jackknife_string = " ({:.2f})".format(r_se_jackknife)
+            else:
+                r_se_jackknife_string= ""
+        else:
+            reg = ss.linregress(df[x],df[y])
+            r_se_jackknife_string= ""
+
+        #### calculate p values based on selected value , default = 0 
+        create_reg_log(reg, log, verbose)
+
+        reg_string = create_reg_string(reg, 
+                    r_se_jackknife_string)
+        
+        ax.text(0.99,0.01, reg_string, va="bottom",ha="right",transform=ax.transAxes,bbox=reg_box,**font_kwargs)
+        
+        ax = create_helper_line(ax, reg[0], is_45_helper_line, helper_line_args, reg_xmin=reg_xmin)
+        ax = create_reg_line(ax, reg, reg_xmin=reg_xmin)
+
+    return ax, reg
+
+#############################################################################################################################################################################
+def create_reg_log(reg,log, verbose):
+    #t_score = (reg[0]-null_beta) / reg[4]
+    #degree = len(df.dropna())-2
+    p =  reg[3]
+    #ss.t.sf(abs(t_score), df=degree)*2
+    log.write(" -Beta = ", reg[0], verbose=verbose)
+    log.write(" -Beta_se = ", reg[4], verbose=verbose)
+    log.write(" -H0 beta =  0",", default p = ", "{:.2e}".format(reg[3]), verbose=verbose)
+    log.write(" -Peason correlation coefficient =  ", "{:.2f}".format(reg[2]), verbose=verbose)
+    log.write(" -r2 =  ", "{:.2f}".format(reg[2]**2), verbose=verbose)
+
+def create_helper_line(ax, 
+                       slope,
+                       is_45_helper_line, 
+                       helper_line_args,
+                       reg_xmin=0):
+    
+    if is_45_helper_line is True:
+        xl,xh=ax.get_xlim()
+        yl,yh=ax.get_ylim()
+        if slope >0:
+            ax.axline([min(xl,yl),min(xl,yl)], [max(xh, yh),max(xh, yh)],zorder=1,**helper_line_args)
+        else:
+            ax.axline([min(xl,yl),-min(xl,yl)], [max(xh, yh),-max(xh, yh)],zorder=1,**helper_line_args)
+
+    return ax
+
+def create_reg_line(ax, reg, reg_xmin=0):
+    xy1 = (reg_xmin,reg[0]*reg_xmin+reg[1])
+    ax.axline(xy1=xy1,slope=reg[0],color="#cccccc",linestyle='--',zorder=1)
+    return ax
+
+def create_reg_string(reg,  
+                      r_se_jackknife_string):
+    p = reg[2]
+    try:
+        p12=str("{:.2e}".format(p)).split("e")[0]
+        pe =str(int("{:.2e}".format(p).split("e")[1]))
+    except:
+        p12="0"
+        pe="0"
+
+    p_text="$p = " + p12 + " \\times  10^{"+pe+"}$"
+    p_latex= f'{p_text}'
+
+    reg_string = "$y =$ "+"{:.2f}".format(reg[1]) +" $+$ "+ "{:.2f}".format(reg[0])+" $x$, "+ p_latex + ", $r =$" +"{:.2f}".format(reg[2])+r_se_jackknife_string
+    
+    return reg_string
+
+def jackknife_r(df,x,y,log,verbose):
+    """Jackknife estimation of se for rsq
+    """
+
+    # dropna
+    df_nona = df.loc[:,[x,y]].dropna()
+    # non-empty entries
+    n=len(df)
+    # assign row number
+    df_nona["_NROW"] = range(n)
+    # a list to store r2
+    r_list=[]
+    # estimate r
+    for i in range(n):
+        # exclude 1 record
+        records_to_use = df_nona["_NROW"]!=i
+        # estimate r
+        reg_jackknife = ss.linregress(df_nona.loc[records_to_use, x],df_nona.loc[records_to_use,y])
+        # add r_i to list
+        r_list.append(reg_jackknife[2])
+
+    # convert list to array
+    rs = np.array(r_list)
+    # https://en.wikipedia.org/wiki/Jackknife_resampling
+    r_se = np.sqrt( (n-1)/n * np.sum((rs - np.mean(rs))**2) )
+    log.write(" -R se (jackknife) = {:.2e}".format(r_se), verbose=verbose)
+    return r_se

{gwaslab-3.5.1 → gwaslab-3.5.2}/src/gwaslab/viz_plot_trumpetplot.py

@@ -281,7 +281,7 @@ def plottrumpet(mysumstats,
     sumstats["ABS_BETA"] = sumstats[beta].abs()
 
     ##################################################################################################
-    size_norm = (sumstats["ABS_BETA"].min(), sumstats["ABS_BETA"].max())
+    size_norm = (sumstats[size].min(), sumstats[size].max())
     ## if highlight  ##################################################################################################
     dots = sns.scatterplot(data=sumstats,
                     x=maf,

{gwaslab-3.5.1 → gwaslab-3.5.2/src/gwaslab.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.5.1
+Version: 3.5.2
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/

{gwaslab-3.5.1 → gwaslab-3.5.2}/src/gwaslab.egg-info/SOURCES.txt

@@ -76,6 +76,7 @@ src/gwaslab/viz_plot_qqplot.py
 src/gwaslab/viz_plot_regional2.py
 src/gwaslab/viz_plot_regionalplot.py
 src/gwaslab/viz_plot_rg_heatmap.py
+src/gwaslab/viz_plot_scatter_with_reg.py
 src/gwaslab/viz_plot_stackedregional.py
 src/gwaslab/viz_plot_trumpetplot.py
 src/gwaslab.egg-info/PKG-INFO