gwaslab 3.5.6__py3-none-any.whl → 3.5.8__py3-none-any.whl

gwaslab/viz_plot_stackedregional.py

@@ -56,7 +56,7 @@ def plot_stacked_mqq(   objects,
                         gtf=None,
                         gene_track_height=0.5,
                         fig_args=None,
-                        region_hspace=0.05,
+                        region_hspace=0.07,
                         subplot_height=4,
                         region_lead_grids = None,
                         region_lead_grid_line=None,
@@ -86,11 +86,14 @@ def plot_stacked_mqq(   objects,
             if "P" in each_object.data.columns or "MLOG10P" in each_object.data.columns:
                 sumstats_list.append(each_object.data)
                 pm.append("m")
-        else:
+        if type(each_object) is pd.DataFrame:
             if "PIP" in each_object.columns:
                 sumstats_list.append(each_object)
                 pm.append("pip")
                 common_ylabel=False
+            else:
+                sumstats_list.append(each_object)
+                pm.append("m")
     
     if common_ylabel==True:
         rr_ylabel=False
@@ -113,10 +116,10 @@ def plot_stacked_mqq(   objects,
     if region_ld_legends is None:
         region_ld_legends = [0]
     if title_args is None:
-        title_args = {"family":"Arial"}
+        title_args = {"family":font_family}
     else:
         if "family" not in title_args.keys():
-            title_args["family"] = "Arial"
+            title_args["family"] = font_family
 
     if save is not None:
         if type(save) is not bool:
@@ -124,10 +127,17 @@ def plot_stacked_mqq(   objects,
                 if save[-3:]=="pdf" or save[-3:]=="svg":
                     log.write(" -Adjusting options for saving as pdf/svg...",verbose=verbose)
                     fig_args["dpi"]=72
+                    
                     if "scatter_args" not in  mqq_args.keys():
                         mqq_args["scatter_args"]={"rasterized":True}
                     else:
                         mqq_args["scatter_args"]["rasterized"] = True
+
+                    if mode=="r":
+                        if "scatter_args" not in  mqq_args.keys():
+                            mqq_args["scatter_args"]={"rasterized":False}
+                        else:
+                            mqq_args["scatter_args"]["rasterized"] = False
                 else:
                     fig_args["dpi"] = save_args["dpi"]
     # create figure and axes ##################################################################################################################
@@ -363,10 +373,15 @@ def _add_new_y_label(mode, fig, gene_track_height,n_plot,subplot_height ,fontsiz
     gene_track_height_ratio = gene_track_height/(gene_track_height + n_plot*subplot_height)
     ylabel_height = (1 - gene_track_height_ratio)*0.5 + gene_track_height_ratio
     if mode=="r":
-        fig.text(0.08, ylabel_height , "$-log_{10}(P)$", va='center', rotation='vertical',fontsize=fontsize,family=font_family)
+        fig.text(0.08, ylabel_height , "$\mathregular{-log_{10}(P)}$", va='center', rotation='vertical',
+                 fontsize=fontsize,
+                 family=font_family)
+        
         fig.text(0.93, ylabel_height, "Recombination rate(cM/Mb)", va='center', rotation=-90,fontsize=fontsize,family=font_family)
     elif mode=="m":
-        fig.text(0.08, ylabel_height , "$-log_{10}(P)$", va='center', rotation='vertical',fontsize=fontsize,family=font_family)    
+        fig.text(0.08, ylabel_height , "$\mathregular{-log_{10}(P)}$", va='center', rotation='vertical',
+                 fontsize=fontsize,
+                 family=font_family)    
 
 def _sort_args(mqq_args, n_plot):
     mqq_args_for_each_plot={i:{} for i in range(n_plot)}

{gwaslab-3.5.6.dist-info → gwaslab-3.5.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.5.6
+Version: 3.5.8
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -8,7 +8,7 @@ Project-URL: Github, https://github.com/Cloufield/gwaslab
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: <3.11,>=3.9
+Requires-Python: <3.13,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: LICENSE_before_v3.4.39
@@ -25,15 +25,15 @@ Requires-Dist: scikit-allel>=1.3.5
 Requires-Dist: pyensembl==2.2.3
 Requires-Dist: gtfparse==1.3.0
 Requires-Dist: h5py>=3.10.0
+Dynamic: license-file
 
 # GWASLab
 
-<img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/197167760-5f761f5e-5856-4b27-a540-8b9cd90bdadb.png">
+<img width="600" alt="image" src="https://github.com/user-attachments/assets/109262c6-c870-4078-94b5-66cf8c6b13c4" />
 
 ![badge](https://img.shields.io/pypi/v/gwaslab)
 [![Downloads](https://static.pepy.tech/badge/gwaslab)](https://pepy.tech/project/gwaslab)
 ![badge_pip](https://img.shields.io/pypi/dm/gwaslab)
-[![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fcloufield.github.io%2Fgwaslab%2F&count_bg=%2379C83D&title_bg=%23555555&icon=&icon_color=%23E7E7E7&title=hits&edge_flat=false)](https://hits.seeyoufarm.com)
 ![badge_commit_m](https://img.shields.io/github/commit-activity/m/Cloufield/gwaslab)
 
 * A handy Python toolkit for handling GWAS summary statistics (sumstats).
@@ -42,7 +42,7 @@ Requires-Dist: h5py>=3.10.0
 
 Please check GWASLab documentation at [https://cloufield.github.io/gwaslab/](https://cloufield.github.io/gwaslab/)
 
-Note: GWASLab is being updated very frequently for now. I will release the first stable version soon! Please stay tuned.
+Note: GWASLab is being updated very frequently for now. We will release the first stable version soon! Please stay tuned.
 
 Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/gwaslab/KnownIssues/](https://cloufield.github.io/gwaslab/KnownIssues/) .
 
@@ -50,8 +50,10 @@ Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/
 
 ### install via pip
 
+The latest version of GWASLab now supports Python 3.9, 3.10, 3.11, and 3.12.
+
 ```
-pip install gwaslab==3.5.4
+pip install gwaslab==3.5.7
 ```
 
 ```python

gwaslab-3.5.8.dist-info/RECORD

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