gwaslab 3.5.7__py3-none-any.whl → 3.6.0__py3-none-any.whl

gwaslab/util_in_meta_polars.py

@@ -0,0 +1,174 @@
+
+import pandas as pd
+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.g_Sumstats import Sumstats
+import gc
+import polars as pl
+import statsmodels.api as sm
+########################################################################################################################################################################################################################################################################################################################################################
+########################################################################################################################################################################################################################################################################################################################################################
+########################################################################################################################################################################################################################################################################################################################################################
+################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################
+########################################################################################################################################################################################################################################################################################################################################################
+########################################################################################################################################################################################################################################################################################################################################################
+
+def meta_analyze_polars(sumstats_multi,
+                       random_effects=False,
+                       nstudy=1, 
+                       log=Log()):
+    log.write("Start to perform meta-analysis...")
+    ###########################################################################
+    log.write(" -Initiating result DataFrame...")
+    
+    sumstats_multi = sumstats_multi.with_row_index()
+
+    sumstats_multi = sumstats_multi.with_columns(
+        N=pl.lit(0),
+        _BETAW_SUM = pl.lit(0.0),
+        _BETA2W_SUM =pl.lit(0.0),
+        _W_SUM =pl.lit(0.0),
+        _W2_SUM=pl.lit(0.0),
+        _EA_N=pl.lit(0.0),
+        _NEA_N=pl.lit(0.0),
+        DIRECTION =pl.lit(""),
+        BETA=pl.lit(0.0),
+        SE=pl.lit(0.0),
+        DOF =pl.lit(-1),
+        _R2=pl.lit(0.0),
+    )
+
+    for i in range(nstudy):
+        n="N_{}".format(i+1)
+        beta="BETA_{}".format(i+1)
+        se="SE_{}".format(i+1)
+        eaf="EAF_{}".format(i+1)
+        sumstats_multi = sumstats_multi.with_columns(
+        pl.when(pl.col(beta).is_null())  
+        .then(pl.col("N"))  
+        .otherwise(pl.col("N") + pl.col(n))
+        .alias("N")
+        ).with_columns(
+        pl.when(pl.col(beta).is_null())  
+        .then(pl.col("DOF") )  
+        .otherwise(pl.col("DOF") + 1 )
+        .alias("DOF")
+        ).with_columns(   
+        pl.when(pl.col(beta).is_null())  
+        .then(pl.col("_BETA2W_SUM"))  
+        .otherwise(pl.col("_BETA2W_SUM")   +   pl.col(beta)**2 *(1/(pl.col(se)**2))) 
+        .alias("_BETA2W_SUM")
+        ).with_columns(   
+        pl.when(pl.col(beta).is_null())  
+        .then( pl.col("_BETAW_SUM") )  
+        .otherwise(pl.col("_BETAW_SUM") + pl.col(beta)*(1/(pl.col(se)**2)) )
+        .alias("_BETAW_SUM")        
+        ).with_columns(
+        pl.when(pl.col(beta).is_null())  
+        .then( pl.col("_W_SUM") )  
+        .otherwise(pl.col("_W_SUM") + 1/(pl.col(se)**2))   
+        .alias("_W_SUM")   
+        ).with_columns(
+        pl.when(pl.col(beta).is_null())  
+        .then( pl.col("_W2_SUM") )  
+        .otherwise(pl.col("_W2_SUM") +  pl.col("_W_SUM")**2)  
+        .alias("_W2_SUM")   
+        ).with_columns(
+        pl.when(pl.col(beta).is_null())  
+        .then( pl.col("_EA_N") )  
+        .otherwise(pl.col("_EA_N") +  pl.col(n)*pl.col(eaf))  
+        .alias("_EA_N")   
+        ).with_columns(
+        pl.when(pl.col(beta).is_null())  
+        .then( pl.col("_NEA_N") )  
+        .otherwise(pl.col("_EA_N") +  pl.col(n)*(1-pl.col(eaf)))  
+        .alias("_NEA_N")   
+        ).with_columns(
+        pl.when(pl.col(beta) <0 )  
+        .then( pl.col("DIRECTION") +"-" )  
+        .otherwise( pl.col("DIRECTION") )  
+        .alias("DIRECTION")   
+        ).with_columns(
+        pl.when(pl.col(beta) >0 )  
+        .then( pl.col("DIRECTION") +"-" )  
+        .otherwise( pl.col("DIRECTION") )  
+        .alias("DIRECTION")   
+        ).with_columns(
+        pl.when(pl.col(beta) ==0 )  
+        .then( pl.col("DIRECTION") +"0" )  
+        .otherwise( pl.col("DIRECTION") )  
+        .alias("DIRECTION")   
+        ).with_columns(
+        pl.when(pl.col(beta).is_null() )  
+        .then( pl.col("DIRECTION") +"?" )  
+        .otherwise( pl.col("DIRECTION") )  
+        .alias("DIRECTION")   
+        )
+        
+    sumstats_multi = sumstats_multi.with_columns(
+        BETA = pl.col("_BETAW_SUM") / pl.col("_W_SUM"),
+        EAF = pl.col("_EA_N") / (pl.col("_EA_N") + pl.col("_NEA_N")),
+        SE = (1/pl.col("_W_SUM")).sqrt(),
+        Q = pl.col("_BETA2W_SUM") - (pl.col("_BETAW_SUM")**2/pl.col("_W_SUM"))
+    )
+
+    sumstats_multi = sumstats_multi.with_columns(
+        Z = pl.col("BETA") / pl.col("SE")
+    ).with_columns(
+        P = pl.col("Z").map_batches(lambda x: pl.Series(2*norm.sf(x.abs())))
+    )
+
+    if random_effects==True:
+        sumstats_multi = sumstats_multi.with_columns(
+            _R2 = (pl.col("Q") - pl.col("DOF")) / (pl.col("_W_SUM") - (pl.col("_W2_SUM")/pl.col("_W_SUM")))
+        ).with_columns(
+           pl.when(pl.col("_R2")<0 )  
+            .then( pl.lit(0)  )  
+            .otherwise( pl.col("_R2") )  
+            .alias("_R2")   
+        )
+        
+        sumstats_multi = sumstats_multi.with_columns(
+            _BETAW_SUM_R = pl.lit(0.0),
+            _W_SUM_R =pl.lit(0.0),
+            BETA_RANDOM =pl.col("BETA"),
+            SE_RANDOM =  pl.col("SE")
+            )
+
+
+        
+        for i in range(nstudy):
+            n="N_{}".format(i+1)
+            beta="BETA_{}".format(i+1)
+            se="SE_{}".format(i+1)
+            eaf="EAF_{}".format(i+1)
+            
+            sumstats_multi = sumstats_multi.with_columns(
+                pl.when( pl.col(beta).is_null() )  
+                .then(pl.col("_BETAW_SUM_R"))  
+                .otherwise(pl.col("_BETAW_SUM_R") + pl.col(beta)*(1/ (pl.col(se)**2 + pl.col("_R2")) ))
+                .alias("_BETAW_SUM_R")
+            ).with_columns(
+                pl.when( pl.col(beta).is_null() )  
+                .then(pl.col("_W_SUM_R") )  
+                .otherwise( pl.col("_W_SUM_R")  + 1/(pl.col(se)**2 + pl.col("_R2") ) )
+                .alias("_W_SUM_R")
+            )
+
+        sumstats_multi = sumstats_multi.with_columns(
+            BETA_RANDOM = (pl.col("_BETAW_SUM_R") / pl.col("_W_SUM_R"))
+        ).with_columns(
+            SE_RANDOM = ( (1/pl.col("_W_SUM_R")).sqrt() )
+        ).with_columns(
+            Z_RANDOM = pl.col("BETA_RANDOM") /  pl.col("SE_RANDOM")
+        ).with_columns(
+            P_RANDOM = pl.col("Z_RANDOM").map_batches(lambda x: pl.Series(2*norm.sf(x.abs()))
+        )
+    )
+
+    sumstats_multi = sumstats_multi.select(pl.all().exclude("^_.*$|\w+_[\d]+$")        )
+    log.write("Finished performing meta-analysis.")
+    return sumstats_multi

gwaslab/viz_aux_annotate_plot.py

@@ -26,6 +26,7 @@ def annotate_single(
     anno_alias,
     anno_style,
     anno_args,
+    anno_args_single,
     arm_scale,
     anno_max_iter,
     arm_scale_d,
@@ -216,13 +217,23 @@ def annotate_single(
             if anno_style == "tight" :
                 anno_default["rotation"] = 90
             ################################################################################################################################
-
+            # anno args for all
             for key,value in anno_args.items():
                 anno_default[key]=value
-            if len(highlight_i) >0 and highlight_chrpos==True:
+            
+            # anno args for highlight group
+            if len(highlight_i) >0:
                 if row["i"] in highlight_i:
                     for key,value in highlight_anno_args.items():
                         anno_default[key]=value
+            
+            # anno args for specifc
+            #try:
+            if row[snpid] in anno_args_single.keys():
+                for key,value in anno_args_single[row[snpid]].items():
+                    anno_default[key]=value
+            #except:
+            #    pass
             ################################################################################################################################
             if anno_adjust==True:
                 if  _invert==False:

gwaslab/viz_plot_compare_effect.py

@@ -51,11 +51,12 @@ def compare_effect(path1,
                    reg_box=None,
                    is_reg=True,
                    fdr=False,
+                   reg_text="full",
                    allele_match=False,
                    r_se=False,
                    is_45_helper_line=True,
                    legend_mode="full",
-                   legend_title=r'$ P < 5 x 10^{-8}$ in:',
+                   legend_title=r'$\mathregular{ P < 5 x 10^{-8}}$ in:',
                    legend_title2=r'Heterogeneity test:',
                    legend_pos='upper left',
                    scatterargs=None,
@@ -85,12 +86,12 @@ def compare_effect(path1,
         scaled1 = True
         scaled2 = True
 
-    if legend_title== r'$ P < 5 x 10^{-8}$ in:' and sig_level!=5e-8:
+    if legend_title== r'$\mathregular{ P < 5 x 10^{-8}}$ in:' and sig_level!=5e-8:
         
         exponent = math.floor(math.log10(sig_level))
         mantissa = sig_level / 10**exponent
 
-        legend_title =  '$ P < {} x 10^{{{}}}$ in:'.format(mantissa, exponent)
+        legend_title =  '$\mathregular{ P < {} x 10^{{{}}}}$ in:'.format(mantissa, exponent)
 
     if is_q_mc=="fdr" or is_q_mc=="bon":
         is_q = True
@@ -100,6 +101,8 @@ def compare_effect(path1,
     if save_args is None:
         save_args = {"dpi":300,"facecolor":"white"}
     if reg_box is None:
+        reg_box= None
+    elif reg_box==True:
         reg_box = dict(boxstyle='round', facecolor='white', alpha=1,edgecolor="grey")
     if sep is None:
         sep = ["\t","\t"]
@@ -116,7 +119,7 @@ def compare_effect(path1,
     if helper_line_args is None:
         helper_line_args={"color":'black', "linestyle":'-',"lw":1}
     if plt_args is None:
-        plt_args={"figsize":(8,8),"dpi":300}
+        plt_args={"figsize":(7,7),"dpi":300}
     if scatterargs is None:
         scatterargs={"s":20}
     if label is None:
@@ -487,9 +490,23 @@ def compare_effect(path1,
         ax.spines[spine].set_visible(False)
     
     ###regression line##############################################################################################################################
-    ax = confire_regression_line(is_reg,reg_box, sig_list_merged, ax, mode,xl,yl,xh,yh, null_beta, r_se, 
-                            is_45_helper_line,helper_line_args, font_kwargs,
-                            log, verbose)
+    ax = configure_regression_line(is_reg=is_reg,
+                                 reg_text=reg_text,
+                                 reg_box=reg_box, 
+                                 sig_list_merged=sig_list_merged, 
+                                 ax=ax, 
+                                 mode=mode,
+                                 xl=xl,
+                                 yl=yl,
+                                 xh=xh,
+                                 yh=yh, 
+                                 null_beta=null_beta, 
+                                 r_se=r_se, 
+                                 is_45_helper_line=is_45_helper_line,
+                                 helper_line_args=helper_line_args, 
+                                 font_kwargs=font_kwargs,
+                                 log=log, 
+                                 verbose=verbose)
         
     
     ax.set_xlabel(xylabel_prefix+label[0],**font_kwargs)
@@ -1128,9 +1145,23 @@ def scatter_annotation(ax, sig_list_merged,anno, anno_het, is_q, mode,
     return ax
 
 
-def confire_regression_line(is_reg, reg_box, sig_list_merged,  ax, mode,xl,yl,xh,yh, null_beta, r_se, 
-                            is_45_helper_line,helper_line_args, font_kwargs,
-                            log, verbose):
+def configure_regression_line(is_reg, 
+                              reg_box, 
+                              reg_text,
+                              sig_list_merged,  
+                              ax, 
+                              mode,
+                              xl,
+                              yl,
+                              xh,
+                              yh, 
+                              null_beta, 
+                              r_se, 
+                            is_45_helper_line,
+                            helper_line_args, 
+                            font_kwargs,
+                            log, 
+                            verbose):
     if len(sig_list_merged)<3: is_reg=False
     if is_reg is True:
         if mode=="beta" or mode=="BETA" or mode=="Beta":
@@ -1149,8 +1180,8 @@ def confire_regression_line(is_reg, reg_box, sig_list_merged,  ax, mode,xl,yl,xh
 
         #### calculate p values based on selected value , default = 0 
         log.write(" -Calculating p values based on given null slope :",null_beta, verbose=verbose)
-        t_score = (reg[0]-null_beta) / reg[4]
-        degree = len(sig_list_merged.dropna())-2
+        #t_score = (reg[0]-null_beta) / reg[4]
+        #degree = len(sig_list_merged.dropna())-2
         p =  reg[3]
         #ss.t.sf(abs(t_score), df=degree)*2
         log.write(" -Beta = ", reg[0], verbose=verbose)
@@ -1174,9 +1205,25 @@ def confire_regression_line(is_reg, reg_box, sig_list_merged,  ax, mode,xl,yl,xh
             except:
                 p12="0"
                 pe="0"
-            p_text="$p = " + p12 + " \\times  10^{"+pe+"}$"
+            if p > 1e-300:
+                p_text="$\mathregular{p = " + p12 + " \\times  10^{"+pe+"}}$"
+            else:
+                p_text="$\mathregular{p < 1 \\times 10^{-300}}$"
             p_latex= f'{p_text}'
-            ax.text(0.98,0.02,"$y =$ "+"{:.2f}".format(reg[1]) +" $+$ "+ "{:.2f}".format(reg[0])+" $x$, "+ p_latex + ", $r =$" +"{:.2f}".format(reg[2])+r_se_jackknife_string, va="bottom",ha="right",transform=ax.transAxes, bbox=reg_box, **font_kwargs)
+
+            if reg_text=="full":
+                reg_string = "y = "+"{:.2f}".format(reg[1]) +" + "+ "{:.2f}".format(reg[0])+" x, "+ p_latex + ", r = " +"{:.2f}".format(reg[2])+r_se_jackknife_string
+                ax.text(0.98,0.02,
+                        reg_string,
+                        va="bottom",ha="right",transform=ax.transAxes, bbox=reg_box, **font_kwargs)
+            elif reg_text=="r":
+                reg_string ="r = " +"{:.2f}".format(reg[2])+r_se_jackknife_string
+                ax.text(0.98,0.02,
+                        reg_string, va="bottom",ha="right",transform=ax.transAxes, bbox=reg_box, **font_kwargs)
+            elif reg_text=="r2":
+                reg_string = "$\mathregular{r^{2}} = " +"{:.2f}".format(reg[2]**2)
+                ax.text(0.98,0.02,
+                        reg_string, va="bottom",ha="right",transform=ax.transAxes, bbox=reg_box, **font_kwargs)
         else:
             #if regression coeeficient <0 : auxiliary line slope = -1
             if is_45_helper_line is True:
@@ -1191,9 +1238,25 @@ def confire_regression_line(is_reg, reg_box, sig_list_merged,  ax, mode,xl,yl,xh
             except:
                 p12="0"
                 pe="0"
-            p_text="$p = " + p12 + " \\times  10^{"+pe+"}$"
+
+            if p > 1e-300:
+                p_text="$\mathregular{p = " + p12 + " \\times  10^{"+pe+"}}$"
+            else:
+                p_text="$\mathregular{p < 1 \\times 10^{-300}}$"
             p_latex= f'{p_text}'
-            ax.text(0.98,0.02,"$y =$ "+"{:.2f}".format(reg[1]) +" $-$ "+ "{:.2f}".format(abs(reg[0]))+" $x$, "+ p_latex + ", $r =$" +"{:.2f}".format(reg[2])+r_se_jackknife_string, va="bottom",ha="right",transform=ax.transAxes,bbox=reg_box,**font_kwargs)
+
+            if reg_text=="full":
+                ax.text(0.98,0.02,
+                    "y = "+"{:.2f}".format(reg[1]) +" - "+ "{:.2f}".format(abs(reg[0]))+" x, "+ p_latex + ", r = " +"{:.2f}".format(reg[2])+r_se_jackknife_string, 
+                    va="bottom",ha="right",transform=ax.transAxes,bbox=reg_box,**font_kwargs)
+            elif reg_text=="r":
+                ax.text(0.98,0.02,
+                        "r = " +"{:.2f}".format(reg[2])+r_se_jackknife_string, 
+                        va="bottom",ha="right",transform=ax.transAxes, bbox=reg_box, **font_kwargs)
+            elif reg_text=="r2":
+                ax.text(0.98,0.02,
+                        "$\mathregular{r^{2}} = " +"{:.2f}".format(reg[2]**2), 
+                        va="bottom",ha="right",transform=ax.transAxes, bbox=reg_box, **font_kwargs)
             
         if mode=="beta" or mode=="BETA" or mode=="Beta":
             middle = sig_list_merged["EFFECT_1"].mean()
@@ -1216,7 +1279,8 @@ def configure_legend(fig, ax, legend_mode, is_q, is_q_mc, legend_elements, legen
             "handletextpad":0.8,
             "edgecolor":"grey",
             "borderpad":0.3,
-            "alignment":"left"
+            "alignment":"left",
+            "frameon":False
         }
 
     if legend_args is not None:
@@ -1227,14 +1291,14 @@ def configure_legend(fig, ax, legend_mode, is_q, is_q_mc, legend_elements, legen
         title_proxy = Rectangle((0,0), 0, 0, color='w',label=legend_title)
         title_proxy2 = Rectangle((0,0), 0, 0, color='w',label=legend_title2)
         if is_q_mc=="fdr":
-            het_label_sig = r"$FDR_{het} < $" + "${}$".format(q_level)
-            het_label_sig2 = r"$FDR_{het} > $" + "${}$".format(q_level)
+            het_label_sig = r"$\mathregular{FDR_{het} < }$" + "{}".format(q_level)
+            het_label_sig2 = r"$\mathregular{FDR_{het} > }$" + "{}".format(q_level)
         elif is_q_mc=="bon":
-            het_label_sig = r"$P_{het,bon} < $" + "${}$".format(q_level)
-            het_label_sig2 = r"$P_{het,bon} > $" + "${}$".format(q_level)
+            het_label_sig = r"$\mathregular{P_{het,bon} < }$" + "{}".format(q_level)
+            het_label_sig2 = r"$\mathregular{P_{het,bon} > }$" + "{}".format(q_level)
         else:
-            het_label_sig = r"$P_{het} < $" + "${}$".format(q_level)
-            het_label_sig2 = r"$P_{het} > $" + "${}$".format(q_level)
+            het_label_sig = r"$\mathregular{P_{het} < }$" + "{}".format(q_level)
+            het_label_sig2 = r"$\mathregular{P_{het} > }$" + "{}".format(q_level)
         het_sig = Rectangle((0,0), 0, 0, facecolor='#cccccc',edgecolor="black", linewidth=1, label=het_label_sig)
         het_nonsig = Rectangle((0,0), 0, 0, facecolor='#cccccc',edgecolor="white",linewidth=1, label=het_label_sig2)
         

gwaslab/viz_plot_credible_sets.py

@@ -9,39 +9,56 @@ 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
+import copy
 
-def _plot_cs(pipcs,
-            region, 
+def _plot_cs(pipcs_raw,
+            region=None, 
+            locus=None,
             figax=None, 
             _posdiccul=None,
             xtick_chr_dict=None,
             pip="PIP",
             onlycs=False,
+            pos="POS",
+            chrom="CHR",
             cs="CREDIBLE_SET_INDEX",
+            cs_category = "CS_CATEGORY",
             marker_size=(45,85),
             fontsize = 12,
             font_family = "Arial",
-            legend_title="Credible sets",
+            legend_title="Credible set",
+            fig_args=None,
             log=Log(),
             verbose=True,
             **kwargs):
         '''
         pipcs : a DataFrame of finemapping results
         '''   
+        pipcs = pipcs_raw.copy()
         ## parameters ############################# 
         if xtick_chr_dict is None:         
                 xtick_chr_dict = get_number_to_chr()
-
+        if fig_args is None:
+                fig_args={"figsize":(15,5),"dpi":400}
         scatter_kwargs =   _extract_kwargs("scatter", dict(), locals())
 
         region_marker_shapes = ['o', '^','s','D','*','P','X','h','8']
         region_ld_colors_m = ["grey","#E51819","green","#F07818","#AD5691","yellow","purple"]
         
-
-        ## filter data #############################
-        pipcs = _filter_region(pipcs, region)
+        if region is not None:
+                ## filter data #############################
+                pipcs = _filter_region(pipcs, region)
+                log.write(" -Loading PIP and CS for variants in the region :{}".format(region))
+        
+        if locus is not None:
+                pipcs = pipcs.loc[pipcs["LOCUS"] == locus,:].copy()
+                log.write(" -Loading PIP and CS for variants in the locus :{}".format(region))
+                if region is None:
+                        region = (pipcs[chrom].iloc[0],pipcs[pos].min(),pipcs[pos].max())
+                        log.write(" -Extracted region:{}".format(region))
         if onlycs ==True:
                 pipcs = pipcs.loc[pipcs[cs]>0,:]
+                log.write(" -Loading only variants in CS...")
 
         pipcs[cs] = pipcs[cs].astype("string")
 
@@ -50,7 +67,7 @@ def _plot_cs(pipcs,
                 ax=figax[1]
                 fig=figax[0]
         else:
-                fig, ax = plt.subplots()
+                fig, ax = plt.subplots(**fig_args)
 
         # assign i
         pipcs,chrom_df=_quick_assign_i_with_rank(pipcs,  chrpad=0.00, 
@@ -58,12 +75,17 @@ def _plot_cs(pipcs,
                                                 chrom="CHR",pos="POS",
                                                 drop_chr_start=False,
                                                 _posdiccul=_posdiccul)
+        
         pipcs = pipcs.sort_values(by=cs,ascending=True)
 
         ## plot ##########################################
         scatter_kwargs["markers"]= {m:region_marker_shapes[i] for i,m in enumerate(pipcs[cs].unique())}
         palette = sns.color_palette(region_ld_colors_m,n_colors=pipcs[cs].nunique()) 
         edgecolor="none"
+        
+        if cs_category in pipcs.columns:
+                cs_category_dic = pipcs.loc[~pipcs[cs_category].isna(), [cs, cs_category]].drop_duplicates().set_index(cs).to_dict()
+                
 
         plot = sns.scatterplot(data=pipcs,
                         x="i",
@@ -75,6 +97,17 @@ def _plot_cs(pipcs,
                         s=marker_size[1],
                         ax=ax,
                         **scatter_kwargs)
+        
+        region_step=21
+        region_ticks = list(map('{:.3f}'.format,np.linspace(region[1], region[2], num=region_step).astype("int")/1000000)) 
+        
+        most_left_snp      = pipcs["i"].idxmin()
+        # distance between leftmost variant position to region left bound
+        i_pos_offset = pipcs.loc[most_left_snp,"i"] - pipcs.loc[most_left_snp,pos]
+        ax.set_xticks(np.linspace(i_pos_offset+region[1], i_pos_offset+region[2], num=region_step))
+        ax.set_xticklabels(region_ticks,rotation=45)
+        xlabel = "Chromosome "+str(region[0])+" (MB)"
+        ax.set_xlabel(xlabel,fontsize=fontsize,family=font_family)
 
         # process legend
         handles, labels = ax.get_legend_handles_labels()
@@ -82,18 +115,29 @@ def _plot_cs(pipcs,
         new_handles = []
         ncol = len(labels)
 
+        ax.tick_params(axis='y', 
+                        labelsize=fontsize,
+                        labelfontfamily=font_family) 
+        
         for i,label in enumerate(labels):
                 if label in [str(j) for j in range(1,10)]:
-                        new_labels.append(labels[i])
+                        if cs_category in pipcs.columns:
+                                new_labels.append("#{} - {}".format(labels[i],cs_category_dic[cs_category][label]) ) 
+                        else:
+                                new_labels.append("#"+labels[i])
                         new_handles.append(handles[i])
         
+        
         ax.legend(labels =new_labels,  
                   handles=new_handles, 
                   loc="upper right", 
                   bbox_to_anchor=(0.995, 0.995), 
                   ncol=1, 
-                  scatterpoints=2, 
+                  markerfirst=False,
+                  scatterpoints=1, 
                   title=legend_title, 
-                  frameon=True)
+                  title_fontproperties={"size":fontsize,"family":font_family},
+                  prop={"size":fontsize,"family":font_family},
+                  frameon=False)
 
         return fig, log

gwaslab/viz_plot_effect.py

@@ -86,6 +86,8 @@ def _plot_effect(to_plot,
                  verbose=True,
                  legend_mode=1,
                  ncol=2,
+                 fontsize=12,
+                 font_family="Arial",
                  size=None,
                  hue=None,
                  style=None,
@@ -188,26 +190,28 @@ def _plot_effect(to_plot,
                   **err_kwargs)
     
     ax1.axvline(x=0,linestyle="dashed",c="grey")
-    ax1.set_yticks(to_plot[y], labels = to_plot[y_name])
-    ax1.set_ylabel(ylabel) 
+    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) 
 
     if title is not None:
-        ax1.set_title(title)
+        ax1.set_title(title,fontsize=fontsize, family=font_family)
 
     if eaf_panel==True:
         ax2.barh(y=to_plot[y], width=to_plot[eaf], zorder=100, **eaf_args)
-        ax2.set_xlabel(eaf)
+        ax2.set_xlabel(eaf, fontsize=fontsize, family=font_family)
 
     if snpvar_panel==True:
         ax3.barh(y=to_plot[y], width=to_plot[snpr2], zorder=100,**snpr2_args)
-        ax3.set_xlabel(snpr2)
+        ax3.set_xlabel(snpr2, fontsize=fontsize, family=font_family)
     
     #try:
     if legend_mode==1:
         #if ncols==1:
         sns.move_legend(
             ax1, "upper left",
-            bbox_to_anchor=(1, 1), title=None, frameon=False, bbox_transform = axes[-1].transAxes
+            bbox_to_anchor=(1, 1), title=None, frameon=False, bbox_transform = axes[-1].transAxes, 
+            title_fontproperties={"size":fontsize,"family":font_family},
+            prop={"size":fontsize,"family":font_family}
             )
             #else:
 ##
@@ -269,15 +273,21 @@ def _plot_effect(to_plot,
     #    for legend_row in legend_rows[:-1]:
     #        ax1.add_artist(legend_row)
 
-
-
     if effect_label is not None:
-        ax1.set_xlabel(effect_label)
+        ax1.set_xlabel(effect_label, fontsize=fontsize, family=font_family)
+        ax1.tick_params(axis='x', 
+                        labelsize=fontsize,
+                        labelfontfamily=font_family)
     if eaf_label is not None:
-        ax2.set_xlabel(eaf_label)
+        ax2.set_xlabel(eaf_label, fontsize=fontsize, family=font_family)
+        ax2.tick_params(axis='x', 
+                        labelsize=fontsize,
+                        labelfontfamily=font_family)
     if snpr2_label is not None:
-        ax3.set_xlabel(snpr2_label)
-
+        ax3.set_xlabel(snpr2_label, fontsize=fontsize, family=font_family)
+        ax3.tick_params(axis='x', 
+                        labelsize=fontsize,
+                        labelfontfamily=font_family)
     save_figure(fig, save, keyword="forest",save_args=save_kwargs, log=log, verbose=verbose)   
     
     return fig

gwaslab/viz_plot_miamiplot2.py

@@ -301,6 +301,7 @@ def plot_miami2(
     ax5l, ax5r = ax1.get_xlim()
     ax1.set_xlim([min(ax1l,ax5l), max(ax1r,ax5r)])
     ax5.set_xlim([min(ax1l,ax5l), max(ax1r,ax5r)])
+    
     #####################################################################################################################
     ax5.set_xlabel("")
     #ax5.set_xticks(chrom_df)
@@ -317,8 +318,8 @@ def plot_miami2(
     
     ax1.tick_params(axis='x', which='major', pad=xtick_label_pad)
     
-    ax1.set_ylabel("$-log_{10}(P)$",fontsize=fontsize,family=font_family)
-    ax5.set_ylabel("$-log_{10}(P)$",fontsize=fontsize,family=font_family)
+    ax1.set_ylabel("$\mathregular{-log_{10}(P)}$",fontsize=fontsize,family=font_family)
+    ax5.set_ylabel("$\mathregular{-log_{10}(P)}$",fontsize=fontsize,family=font_family)
     
     ax1.set_title(titles[0],y=titles_pad_adjusted[0],family=font_family)
     ax5.set_title(titles[1],y=titles_pad_adjusted[1],family=font_family)