gwaslab 3.5.8__tar.gz → 3.6.0__tar.gz

{gwaslab-3.5.8/src/gwaslab.egg-info → gwaslab-3.6.0}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.5.8
+Version: 3.6.0
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
 Project-URL: Github, https://github.com/Cloufield/gwaslab
 Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: MIT License
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent
 Requires-Python: <3.13,>=3.9
 Description-Content-Type: text/markdown
@@ -36,43 +36,63 @@ Dynamic: license-file
 ![badge_pip](https://img.shields.io/pypi/dm/gwaslab)
 ![badge_commit_m](https://img.shields.io/github/commit-activity/m/Cloufield/gwaslab)
 
-* A handy Python toolkit for handling GWAS summary statistics (sumstats).
+* A handy Python-based toolkit for handling GWAS summary statistics (sumstats).
 * Each process is modularized and can be customized to your needs.
 * Sumstats-specific manipulations are designed as methods of a Python object, `gwaslab.Sumstats`.
 
-Please check GWASLab documentation at [https://cloufield.github.io/gwaslab/](https://cloufield.github.io/gwaslab/)
+## Installation
 
-Note: GWASLab is being updated very frequently for now. We will release the first stable version soon! Please stay tuned.
+### install via pip
 
-Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/gwaslab/KnownIssues/](https://cloufield.github.io/gwaslab/KnownIssues/) .
+The latest version of GWASLab now supports Python 3.9, 3.10, 3.11, and 3.12.
 
-## Install
+```bash
+pip install gwaslab
+```
 
-### install via pip
+### install in conda environment
 
-The latest version of GWASLab now supports Python 3.9, 3.10, 3.11, and 3.12.
+Create a Python 3.9, 3.10, 3.11 or 3.12 environment and install gwaslab using pip:
+
+```bash
+conda env create -n gwaslab -c conda-forge python=3.12
+
+conda activate gwaslab
 
+pip install gwaslab
 ```
-pip install gwaslab==3.5.7
+
+or create a new environment using yml file [environment.yml](https://github.com/Cloufield/gwaslab/blob/main/environment.yml)
+
+```bash
+conda env create -n gwaslab -f environment.yml
 ```
 
+### install using docker (deprecated)
+
+A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main/docker/Dockerfile) for building local images.
+
+## Quick start
+
 ```python
+
 import gwaslab as gl
+
 # load plink2 output
-mysumstats = gl.Sumstats("t2d_bbj.txt.gz", fmt="plink2")
+mysumstats = gl.Sumstats("sumstats.txt.gz", fmt="plink2")
 
-# load sumstats with auto mode (auto-detecting common headers) 
+# or load sumstats with auto mode (auto-detecting commonly used headers) 
 # assuming ALT/A1 is EA, and frq is EAF
-mysumstats = gl.Sumstats("t2d_bbj.txt.gz", fmt="auto")
+mysumstats = gl.Sumstats("sumstats.txt.gz", fmt="auto")
 
 # or you can specify the columns:
-mysumstats = gl.Sumstats("t2d_bbj.txt.gz",
+mysumstats = gl.Sumstats("sumstats.txt.gz",
              snpid="SNP",
              chrom="CHR",
              pos="POS",
              ea="ALT",
              nea="REF",
-             neaf="Frq",
+             eaf="Frq",
              beta="BETA",
              se="SE",
              p="P",
@@ -85,26 +105,9 @@ mysumstats.plot_mqq()
 ...
 ```
 
-### install in conda environment
-
-Create a Python 3.9 environment and install gwaslab using pip:
-
-```
-conda env create -n gwaslab_test -c conda-forge python=3.9
-conda activate gwaslab
-pip install gwaslab==3.4.45
-```
-
-or create a new environment using yml file [environment_3.4.40.yml](https://github.com/Cloufield/gwaslab/blob/main/environment_3.4.40.yml)
-
-```
-conda env create -n gwaslab -f environment_3.4.40.yml
-```
-
-
-### install using docker
+## Documentation and tutorials
 
-A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main/docker/Dockerfile) for building local images.
+Documentation and tutorials for GWASLab are avaiable at [here](https://cloufield.github.io/gwaslab/).
 
 ## Functions
 
@@ -151,7 +154,7 @@ A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main
 - Scatter plot: allele frequency comparison 
 - Scatter plot: trumpet plot (plot of MAF and effect size with power lines)
 
-### Visualization Examples
+#### Visualization Examples
 
 <img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/233836639-34b03c47-5a59-4fd4-9677-5e13b02aab15.png">
 <img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/197393168-e3e7076f-2801-4d66-9526-80778d44f3da.png">
@@ -167,42 +170,15 @@ A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main
 - Sumstats summary: give you a quick overview of the sumstats. 
 - ...
 
-## Requirements (deprecated)
-
-environment.yml
+## Issues
 
-```
-name: gwaslab
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - python=3.8.16=h7a1cb2a_3
-  - jupyter==1.0.0
-  - pip==23.1.2
-  - pip:
-      - adjusttext==0.8
-      - biopython==1.81
-      - gwaslab==3.4.16
-      - liftover==1.1.16
-      - matplotlib==3.7.1
-      - numpy==1.24.2
-      - pandas==1.4.4
-      - scikit-allel==1.3.5
-      - scikit-learn==1.2.2
-      - scipy==1.10.1
-      - seaborn==0.11.2
-      - statsmodels==0.13
-      - adjustText==0.8
-      - pysam==0.19
-      - pyensembl==2.2.3
-      - h5py==3.10.0
-```
+- GWASLab is currently under active development, with frequent updates.
+- Note: Known issues are documented at https://cloufield.github.io/gwaslab/KnownIssues/.
 
 ## How to cite
 - GWASLab preprint: He, Y., Koido, M., Shimmori, Y., Kamatani, Y. (2023). GWASLab: a Python package for processing and visualizing GWAS summary statistics. Preprint at Jxiv, 2023-5. https://doi.org/10.51094/jxiv.370
 
-## Sample Data
+## Sample data used for tutorial
 - Sample GWAS data used in GWASLab is obtained from: http://jenger.riken.jp/ (Suzuki, Ken, et al. "Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population." Nature genetics 51.3 (2019): 379-386.).
 
 ## Acknowledgement

{gwaslab-3.5.8 → gwaslab-3.6.0}/README.md

@@ -7,43 +7,63 @@
 ![badge_pip](https://img.shields.io/pypi/dm/gwaslab)
 ![badge_commit_m](https://img.shields.io/github/commit-activity/m/Cloufield/gwaslab)
 
-* A handy Python toolkit for handling GWAS summary statistics (sumstats).
+* A handy Python-based toolkit for handling GWAS summary statistics (sumstats).
 * Each process is modularized and can be customized to your needs.
 * Sumstats-specific manipulations are designed as methods of a Python object, `gwaslab.Sumstats`.
 
-Please check GWASLab documentation at [https://cloufield.github.io/gwaslab/](https://cloufield.github.io/gwaslab/)
+## Installation
 
-Note: GWASLab is being updated very frequently for now. We will release the first stable version soon! Please stay tuned.
+### install via pip
 
-Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/gwaslab/KnownIssues/](https://cloufield.github.io/gwaslab/KnownIssues/) .
+The latest version of GWASLab now supports Python 3.9, 3.10, 3.11, and 3.12.
 
-## Install
+```bash
+pip install gwaslab
+```
 
-### install via pip
+### install in conda environment
 
-The latest version of GWASLab now supports Python 3.9, 3.10, 3.11, and 3.12.
+Create a Python 3.9, 3.10, 3.11 or 3.12 environment and install gwaslab using pip:
+
+```bash
+conda env create -n gwaslab -c conda-forge python=3.12
+
+conda activate gwaslab
 
+pip install gwaslab
 ```
-pip install gwaslab==3.5.7
+
+or create a new environment using yml file [environment.yml](https://github.com/Cloufield/gwaslab/blob/main/environment.yml)
+
+```bash
+conda env create -n gwaslab -f environment.yml
 ```
 
+### install using docker (deprecated)
+
+A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main/docker/Dockerfile) for building local images.
+
+## Quick start
+
 ```python
+
 import gwaslab as gl
+
 # load plink2 output
-mysumstats = gl.Sumstats("t2d_bbj.txt.gz", fmt="plink2")
+mysumstats = gl.Sumstats("sumstats.txt.gz", fmt="plink2")
 
-# load sumstats with auto mode (auto-detecting common headers) 
+# or load sumstats with auto mode (auto-detecting commonly used headers) 
 # assuming ALT/A1 is EA, and frq is EAF
-mysumstats = gl.Sumstats("t2d_bbj.txt.gz", fmt="auto")
+mysumstats = gl.Sumstats("sumstats.txt.gz", fmt="auto")
 
 # or you can specify the columns:
-mysumstats = gl.Sumstats("t2d_bbj.txt.gz",
+mysumstats = gl.Sumstats("sumstats.txt.gz",
              snpid="SNP",
              chrom="CHR",
              pos="POS",
              ea="ALT",
              nea="REF",
-             neaf="Frq",
+             eaf="Frq",
              beta="BETA",
              se="SE",
              p="P",
@@ -56,26 +76,9 @@ mysumstats.plot_mqq()
 ...
 ```
 
-### install in conda environment
-
-Create a Python 3.9 environment and install gwaslab using pip:
-
-```
-conda env create -n gwaslab_test -c conda-forge python=3.9
-conda activate gwaslab
-pip install gwaslab==3.4.45
-```
-
-or create a new environment using yml file [environment_3.4.40.yml](https://github.com/Cloufield/gwaslab/blob/main/environment_3.4.40.yml)
-
-```
-conda env create -n gwaslab -f environment_3.4.40.yml
-```
-
-
-### install using docker
+## Documentation and tutorials
 
-A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main/docker/Dockerfile) for building local images.
+Documentation and tutorials for GWASLab are avaiable at [here](https://cloufield.github.io/gwaslab/).
 
 ## Functions
 
@@ -122,7 +125,7 @@ A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main
 - Scatter plot: allele frequency comparison 
 - Scatter plot: trumpet plot (plot of MAF and effect size with power lines)
 
-### Visualization Examples
+#### Visualization Examples
 
 <img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/233836639-34b03c47-5a59-4fd4-9677-5e13b02aab15.png">
 <img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/197393168-e3e7076f-2801-4d66-9526-80778d44f3da.png">
@@ -138,42 +141,15 @@ A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main
 - Sumstats summary: give you a quick overview of the sumstats. 
 - ...
 
-## Requirements (deprecated)
-
-environment.yml
+## Issues
 
-```
-name: gwaslab
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - python=3.8.16=h7a1cb2a_3
-  - jupyter==1.0.0
-  - pip==23.1.2
-  - pip:
-      - adjusttext==0.8
-      - biopython==1.81
-      - gwaslab==3.4.16
-      - liftover==1.1.16
-      - matplotlib==3.7.1
-      - numpy==1.24.2
-      - pandas==1.4.4
-      - scikit-allel==1.3.5
-      - scikit-learn==1.2.2
-      - scipy==1.10.1
-      - seaborn==0.11.2
-      - statsmodels==0.13
-      - adjustText==0.8
-      - pysam==0.19
-      - pyensembl==2.2.3
-      - h5py==3.10.0
-```
+- GWASLab is currently under active development, with frequent updates.
+- Note: Known issues are documented at https://cloufield.github.io/gwaslab/KnownIssues/.
 
 ## How to cite
 - GWASLab preprint: He, Y., Koido, M., Shimmori, Y., Kamatani, Y. (2023). GWASLab: a Python package for processing and visualizing GWAS summary statistics. Preprint at Jxiv, 2023-5. https://doi.org/10.51094/jxiv.370
 
-## Sample Data
+## Sample data used for tutorial
 - Sample GWAS data used in GWASLab is obtained from: http://jenger.riken.jp/ (Suzuki, Ken, et al. "Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population." Nature genetics 51.3 (2019): 379-386.).
 
 ## Acknowledgement

{gwaslab-3.5.8 → gwaslab-3.6.0}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gwaslab"
-version = "3.5.8"
+version = "3.6.0"
 authors = [
   { name="Yunye", email="yunye@gwaslab.com" },
 ]
@@ -34,7 +34,7 @@ dependencies = [
 requires-python = ">=3.9,<3.13"
 classifiers = [
     "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: MIT License",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
     "Operating System :: OS Independent",
 ]
 

{gwaslab-3.5.8 → gwaslab-3.6.0}/src/gwaslab/data/reference.json

@@ -103,7 +103,9 @@
     "13to19":"https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/chain/v1_nflo/chm13v2-hg19.chain",
     "13to38":"https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/chain/v1_nflo/chm13v2-grch38.chain",
     "18to19":"https://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.gz",
-    "18to38":"https://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg38.over.chain.gz"
+    "18to38":"https://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg38.over.chain.gz",
+    "1kg_hm3_hg38_eaf":"https://www.dropbox.com/scl/fi/ymkqfsaec6mwjzlvxsm45/PAN.hapmap3.hg38.EAF.tsv.gz?rlkey=p1auef5y1kk7ui41k6j3s8b0z&dl=1",
+    "1kg_hm3_hg19_eaf":"https://www.dropbox.com/scl/fi/dmv9wtfchv6ahim86d49r/PAN.hapmap3.hg19.EAF.tsv.gz?rlkey=ywne2gj1rlm2nj42q9lt2d99n&dl=1"
 }
 
 

{gwaslab-3.5.8 → gwaslab-3.6.0}/src/gwaslab/g_Sumstats.py

@@ -84,6 +84,8 @@ from gwaslab.util_ex_ldsc import _estimate_rg_by_ldsc
 from gwaslab.util_ex_ldsc import _estimate_h2_cts_by_ldsc
 from gwaslab.util_ex_ldsc import _estimate_partitioned_h2_by_ldsc 
 from gwaslab.util_ex_ldproxyfinder import _extract_ld_proxy
+from gwaslab.util_ex_run_magma import _run_magma
+from gwaslab.util_ex_infer_ancestry import _infer_ancestry
 from gwaslab.bd_get_hapmap3 import gethapmap3
 from gwaslab.util_abf_finemapping import abf_finemapping
 from gwaslab.util_abf_finemapping import make_cs
@@ -674,6 +676,9 @@ class Sumstats():
         fig,outliers = plotdaf(self.data, **kwargs)
         return fig, outliers
     
+    def infer_ancestry(self, **kwargs):
+        self.meta["gwaslab"]["inferred_ancestry"] = _infer_ancestry(self.data, **kwargs)
+
     def plot_gwheatmap(self, **kwargs):
         fig = _gwheatmap(self.data, **kwargs)
         return fig
@@ -882,8 +887,14 @@ class Sumstats():
         if build is None:
             build = self.meta["gwaslab"]["genome_build"]
         insumstats = gethapmap3(self.data.copy(), build=build, verbose=verbose , match_allele=match_allele, how=how )
-        _run_prscs(sst_file = insumstats[["rsID","CHR","POS","EA","NEA","BETA","SE"]], log=self.log, **kwargs)
-
+        _run_prscs(sst_file = insumstats[["rsID","CHR","POS","EA","NEA","BETA","SE"]], 
+                   log=self.log, 
+                   **kwargs)
+    
+    def run_magma(self, build=None, verbose=True, **kwargs):
+        _run_magma(self.data, 
+                   study=self.meta["gwaslab"]["study_name"], 
+                   build=build, verbose=verbose, log=self.log, **kwargs)
 ## LDSC ##############################################################################################
     def estimate_h2_by_ldsc(self, build=None, verbose=True, match_allele=True, how="right", **kwargs):
         if build is None:

{gwaslab-3.5.8 → gwaslab-3.6.0}/src/gwaslab/g_meta.py

@@ -6,7 +6,7 @@ def _init_meta(object="Sumstats"):
                         "gwas_id":"Unknown", 
                         "samples":{
                             "sample_size":"Unknown", 
-                            "sample_ancestry":"European", 
+                            "sample_ancestry":"Unknown", 
                             "ancestry_method":"self-reported|genetically determined", 
                         } ,
                         "trait_description":"Unknown", 
@@ -37,6 +37,7 @@ def _init_meta(object="Sumstats"):
                     "species":"homo sapiens",
                     "genome_build":"99",
                     "sample_prevalence":"Unknown",
+                    "inferred_ancestry":"Unknown",
                     "population_prevalence":"Unknown",
                     "variants":{
                         "variant_number":"Unknown",

{gwaslab-3.5.8 → gwaslab-3.6.0}/src/gwaslab/g_version.py

@@ -15,8 +15,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.5.8",
-   "release_date":"20250424"
+   "version":"3.6.0",
+   "release_date":"20250504"
     }
     return dic   
 

gwaslab-3.6.0/src/gwaslab/util_ex_infer_ancestry.py

@@ -0,0 +1,65 @@
+
+import pandas as pd
+from gwaslab.g_Log import Log
+
+def _infer_ancestry(sumstats, 
+                    ancestry_af=None,
+                    build="19",
+                    log=Log(),
+                    verbose=True):
+    log.write("Start to infer ancestry based on Fst...", verbose=verbose)
+    ref_af = pd.read_csv(ancestry_af, sep="\t")
+    
+    data_af = pd.merge(sumstats[["CHR","POS","EA","NEA","EAF"]] ,ref_af,on=["CHR","POS"],how="inner") 
+
+    log.write(f"  -Estimating Fst using {len(data_af)} variants...", verbose=verbose)
+
+    is_filp = data_af["EA"] == data_af["ALT"]
+    data_af.loc[is_filp, ["EA","NEA"]] = data_af.loc[is_filp, ["NEA","EA"]]
+    data_af.loc[is_filp, "EAF"] = 1 - data_af.loc[is_filp, "EAF"]
+    
+    headers = []
+    for i in ['GBR', 'FIN', 'CHS', 'PUR', 'CDX',
+        'CLM', 'IBS', 'PEL', 'PJL', 'KHV', 'ACB', 'GWD', 'ESN', 'BEB', 'MSL',
+        'STU', 'ITU', 'CEU', 'YRI', 'CHB', 'JPT', 'LWK', 'ASW', 'MXL', 'TSI',
+        'GIH', 'EUR', 'EAS', 'AMR', 'SAS', 'AFR']:
+        headers.append(f"FST_{i}")
+        data_af[f"FST_{i}"] = data_af.apply(lambda x: calculate_fst(x["EAF"], x[i]), axis=1)
+    
+    for i,value in data_af[headers].mean().sort_values().items():
+        log.write( f"  -{i} : {value}", verbose=verbose)
+        
+        closest_ancestry = data_af[headers].mean().sort_values().idxmin()
+
+    log.write(f"  -Closest Ancestry: {closest_ancestry.split('_')[1]}", verbose=verbose)
+    log.write("Finished inferring ancestry.", verbose=verbose)
+    return closest_ancestry.split("_")[1]
+
+def calculate_fst(p_1, p_2):
+    # https://bios1140.github.io/understanding-fst-the-fixation-index.html
+    # calculate q1 and q2
+    q_1 = 1 - p_1
+    q_2 = 1 - p_2
+
+    # calculate total allele frequency
+    p_t = (p_1 + p_2)/2
+    q_t = 1 - p_t
+
+    # calculate expected heterozygosity
+    # first calculate expected heterozygosity for the two populations
+    # pop1
+    hs_1 = 2*p_1*q_1
+    # pop2
+    hs_2 = 2*p_2*q_2
+    # then take the mean of this
+    hs = (hs_1 + hs_2)/2
+
+    # next calculate expected heterozygosity for the metapopulations
+    ht = 2*p_t*q_t
+
+    # calculate fst
+    fst = (ht - hs)/ht
+
+    # return output
+    return fst
+    

gwaslab-3.6.0/src/gwaslab/util_ex_run_magma.py

@@ -0,0 +1,74 @@
+import subprocess
+import os
+import gc
+import pandas as pd
+import numpy as np
+from gwaslab.g_Log import Log
+from gwaslab.util_in_filter_value import _exclude_hla
+
+def _run_magma(sumstats, 
+                magma="magma",
+                study="Study1",
+                exclude_hla=True,
+                window="35,10",
+                id_to_use="rsID",
+                ref=None,
+                ncbi=None,
+                set_annot=None,
+                out="./",
+                delete=True, 
+                ncol="N",
+                build="19",
+                log=Log(), 
+                verbose=True):
+    
+    log.write(" Start to run magma from command line:", verbose=verbose)
+
+    if exclude_hla==True:
+        sumstats = _exclude_hla(sumstats, build =build)
+
+    snploc="{}{}.rsid.chr.pos.tsv".format(out,study)
+    pval="{}{}.rsid.p.n.tsv".format(out, study)
+
+    log.write(f" -writing temp file for --snp-loc:{snploc}", verbose=verbose)
+    sumstats.dropna()[[id_to_use,"CHR","POS"]].rename(columns={id_to_use:"SNP"}).to_csv("{}{}.rsid.chr.pos.tsv".format(out,study),index=None, sep="\t")
+    
+    log.write(f" -writing temp file for --pval:{pval}", verbose=verbose)
+    sumstats.dropna()[[id_to_use,"P","N"]].rename(columns={id_to_use:"SNP"}).to_csv("{}{}.rsid.p.n.tsv".format(out,study),index=None, sep="\t")
+    
+    log.write(f" --annotate window: {window}", verbose=verbose)
+    log.write(f" --gene-loc: {ncbi}", verbose=verbose)
+    log.write(f" --bfile: {ref}", verbose=verbose)
+    log.write(f" Output prefix: {out}", verbose=verbose)
+
+    bash_script=f'''
+
+#!/bin/bash
+
+{magma} --annotate window={window}  --snp-loc {snploc} --gene-loc {ncbi} --out {study}
+
+{magma} --bfile {ref} --pval {pval} ncol={ncol} --gene-annot {study}.genes.annot --out {study}
+
+'''
+    
+    if set_annot is not None:
+        bash_script+=f'''
+{magma} --gene-results {study}.genes.raw --set-annot {set_annot} --out {study}
+'''
+    log.write(f"Script: {bash_script}")
+
+    try:
+        log.write(" Running magma from command line...", verbose=verbose)
+        output = subprocess.check_output(bash_script, stderr=subprocess.STDOUT, shell=True,text=True)
+        output =  output + "\n"
+        
+        if delete == True:
+            os.remove(snploc)
+            os.remove(pval)
+
+    except subprocess.CalledProcessError as e:
+        log.warning("ERROR!")
+        log.write(e.output)
+
+    log.write("Finished running magma.", verbose=verbose)
+

{gwaslab-3.5.8 → gwaslab-3.6.0}/src/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-3.5.8 → gwaslab-3.6.0}/src/gwaslab/viz_plot_mqqplot.py

@@ -154,6 +154,7 @@ def mqqplot(insumstats,
           anno_alias=None,
           anno_d=None,
           anno_args=None,
+          anno_args_single=None,
           anno_style="right",
           anno_fixed_arm_length=None,
           anno_source = "ensembl",
@@ -209,7 +210,9 @@ def mqqplot(insumstats,
           drop_chr_start=False,
           title =None,
           mtitle=None,
+          mtitle_pad=1.08,
           qtitle=None,
+          qtitle_pad=1.08,
           ylabel=None,
           xlabel=None,
           title_pad=1.08, 
@@ -256,6 +259,7 @@ def mqqplot(insumstats,
     anno_alias = _update_args(anno_alias, dict())
     anno_d = _update_args(anno_d,dict())
     anno_args = _update_args(anno_args,dict())
+    anno_args_single = _update_args(anno_args_single,dict())
     arrow_kwargs = _update_args(arrow_kwargs,dict())
 
     colors = _update_arg(colors, ["#597FBD","#74BAD3"])
@@ -1002,7 +1006,7 @@ def mqqplot(insumstats,
 
         
         if mtitle and anno and len(to_annotate)>0: 
-            pad=(ax1.transData.transform((skip, title_pad*maxy))[1]-ax1.transData.transform((skip, maxy)))[1]
+            pad=(ax1.transData.transform((skip, mtitle_pad*maxy))[1]-ax1.transData.transform((skip, maxy)))[1]
             ax1.set_title(mtitle,pad=pad,fontsize=title_fontsize,family=font_family)
         elif mtitle:
             ax1.set_title(mtitle,fontsize=title_fontsize,family=font_family)
@@ -1023,6 +1027,7 @@ def mqqplot(insumstats,
                                 anno_alias=anno_alias,
                                 anno_style=anno_style,
                                 anno_args=anno_args,
+                                anno_args_single=anno_args_single,
                                 arm_scale=arm_scale,
                                 anno_max_iter=anno_max_iter,
                                 arm_scale_d=arm_scale_d,
@@ -1074,6 +1079,7 @@ def mqqplot(insumstats,
                     fontsize=fontsize,
                     font_family=font_family,
                     qtitle=qtitle,
+                    qtitle_pad=qtitle_pad,
                     title_fontsize=title_fontsize,
                     include_chrXYMT=include_chrXYMT,
                     cut_line_color=cut_line_color,
@@ -1106,9 +1112,10 @@ def mqqplot(insumstats,
     # Titles 
     if title and anno and len(to_annotate)>0:
         # increase height if annotation 
-        fig.suptitle(title , fontsize = title_fontsize ,x=0.5, y=1.05)
+        fig.suptitle(title , fontsize = title_fontsize ,x=0.5, y=title_pad)
     else:
-        fig.suptitle(title , fontsize = title_fontsize, x=0.5,y=1)
+        title_pad = title_pad -0.05
+        fig.suptitle(title , fontsize = title_fontsize, x=0.5,y=title_pad)
         ## Add annotation arrows and texts
     
     # Saving figure