diff --git a/.gitignore b/.gitignore
index 2bf8ad9..40e3ceb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -145,3 +145,5 @@ examples/*.csv
 vcfstats-out/
 docs/index.md
 examples/*.svg
+
+/localtests
diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
index b32791b..40b8f28 100644
--- a/docs/CHANGELOG.md
+++ b/docs/CHANGELOG.md
@@ -1,3 +1,7 @@
+# 0.4.2
+
+- 🐛 Fix config file not used correctly (#27)
+
 # 0.4.1
 
 - 📝 Add more examples regarding #20
diff --git a/docs/configfile.md b/docs/configfile.md
index 35fa700..8d69fe2 100644
--- a/docs/configfile.md
+++ b/docs/configfile.md
@@ -25,3 +25,7 @@ ggs = 'theme_bw()'
 devpars = {width = 2000, height = 2000, res = 300}
 
 ```
+
+When you have a configuration file provided, `--title` and `--formula` are optional.
+
+The instances specified by `--title` and `--formula` will be used together with the ones provided in the configuration file.
diff --git a/poetry.lock b/poetry.lock
index ab65cd2..043ea27 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,8 +1,8 @@
 [[package]]
 name = "asttokens"
-version = "2.0.5"
+version = "2.0.8"
 description = "Annotate AST trees with source code positions"
-category = "main"
+category = "dev"
 optional = false
 python-versions = "*"
 
@@ -10,29 +10,21 @@ python-versions = "*"
 six = "*"
 
 [package.extras]
-test = ["astroid", "pytest"]
-
-[[package]]
-name = "atomicwrites"
-version = "1.4.0"
-description = "Atomic file writes."
-category = "dev"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+test = ["astroid (<=2.5.3)", "pytest"]
 
 [[package]]
 name = "attrs"
-version = "21.4.0"
+version = "22.1.0"
 description = "Classes Without Boilerplate"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.5"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
 docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"]
 
 [[package]]
 name = "click"
@@ -90,11 +82,11 @@ optional = false
 python-versions = "*"
 
 [package.extras]
-test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"]
+test = ["hypothesis (==3.55.3)", "flake8 (==3.7.8)"]
 
 [[package]]
 name = "coverage"
-version = "6.4.1"
+version = "6.4.4"
 description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
@@ -127,7 +119,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "cyvcf2"
-version = "0.30.15"
+version = "0.30.16"
 description = "fast vcf parsing with cython + htslib"
 category = "main"
 optional = false
@@ -140,7 +132,7 @@ numpy = "*"
 
 [[package]]
 name = "datar"
-version = "0.8.5"
+version = "0.9.0"
 description = "Port of dplyr and other related R packages in python, using pipda."
 category = "main"
 optional = false
@@ -148,15 +140,15 @@ python-versions = ">=3.7.1,<4.0.0"
 
 [package.dependencies]
 pandas = ">=1.3,<2.0"
-pipda = ">=0.6,<0.7"
+pdtypes = ">=0.0,<0.1"
+pipda = ">=0.7.1,<0.8.0"
 python-simpleconf = {version = ">=0.5,<0.6", extras = ["toml"]}
 
 [package.extras]
-pdtypes = ["pdtypes (>=0.0,<0.1)"]
-scipy = ["scipy (>=1.6,<2.0)"]
-wcwidth = ["wcwidth (>=0.2,<0.3)"]
-slugify = ["python-slugify (>=6,<7)"]
 modin = ["modin (>=0.10,<0.11)"]
+slugify = ["python-slugify (>=6,<7)"]
+wcwidth = ["wcwidth (>=0.2,<0.3)"]
+scipy = ["scipy (>=1.6,<2.0)"]
 
 [[package]]
 name = "descartes"
@@ -182,7 +174,7 @@ inflection = ">=0.5,<0.6"
 
 [[package]]
 name = "executing"
-version = "0.8.3"
+version = "1.0.0"
 description = "Get the currently executing AST node of a frame, and other information"
 category = "main"
 optional = false
@@ -190,7 +182,7 @@ python-versions = "*"
 
 [[package]]
 name = "fonttools"
-version = "4.33.3"
+version = "4.37.1"
 description = "Tools to manipulate font files"
 category = "main"
 optional = false
@@ -239,7 +231,7 @@ python-versions = "*"
 
 [[package]]
 name = "kiwisolver"
-version = "1.4.3"
+version = "1.4.4"
 description = "A fast implementation of the Cassowary constraint solver"
 category = "main"
 optional = false
@@ -260,7 +252,7 @@ regex = ["regex"]
 
 [[package]]
 name = "matplotlib"
-version = "3.5.2"
+version = "3.5.3"
 description = "Python plotting package"
 category = "main"
 optional = false
@@ -275,7 +267,7 @@ packaging = ">=20.0"
 pillow = ">=6.2.0"
 pyparsing = ">=2.2.1"
 python-dateutil = ">=2.7"
-setuptools_scm = ">=4"
+setuptools_scm = ">=4,<7"
 
 [[package]]
 name = "mizani"
@@ -298,7 +290,7 @@ testing = ["flake8", "pytest-cov"]
 
 [[package]]
 name = "numpy"
-version = "1.23.0"
+version = "1.23.3"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
@@ -325,7 +317,7 @@ python-versions = "*"
 
 [[package]]
 name = "pandas"
-version = "1.4.3"
+version = "1.4.4"
 description = "Powerful data structures for data analysis, time series, and statistics"
 category = "main"
 optional = false
@@ -357,31 +349,41 @@ numpy = ">=1.4"
 six = "*"
 
 [package.extras]
-test = ["pytest", "pytest-cov", "scipy"]
+test = ["scipy", "pytest-cov", "pytest"]
+
+[[package]]
+name = "pdtypes"
+version = "0.0.4"
+description = "Show data types for pandas data frames in terminal and notebooks"
+category = "main"
+optional = false
+python-versions = ">=3.7.1,<4.0.0"
+
+[package.dependencies]
+pandas = ">=1.2,<2.0"
 
 [[package]]
 name = "pillow"
-version = "9.1.1"
+version = "9.2.0"
 description = "Python Imaging Library (Fork)"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinx-rtd-theme (>=1.0)", "sphinxext-opengraph"]
+docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"]
 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "pipda"
-version = "0.6.0"
+version = "0.7.1"
 description = "A framework for data piping in python"
 category = "main"
 optional = false
 python-versions = ">=3.7,<4.0"
 
 [package.dependencies]
-diot = ">=0.1,<0.2"
-varname = ">=0.8,<0.9"
+executing = ">=1.0,<2.0"
 
 [[package]]
 name = "plotnine"
@@ -402,7 +404,7 @@ scipy = ">=1.5.0"
 statsmodels = ">=0.12.1"
 
 [package.extras]
-all = ["scikit-learn", "scikit-misc"]
+all = ["scikit-misc", "scikit-learn"]
 
 [[package]]
 name = "plotnine-prism"
@@ -426,14 +428,14 @@ optional = false
 python-versions = ">=3.6"
 
 [package.extras]
-dev = ["pre-commit", "tox"]
-testing = ["pytest", "pytest-benchmark"]
+testing = ["pytest-benchmark", "pytest"]
+dev = ["tox", "pre-commit"]
 
 [[package]]
 name = "pure-eval"
 version = "0.2.2"
 description = "Safely evaluate AST nodes without side effects"
-category = "main"
+category = "dev"
 optional = false
 python-versions = "*"
 
@@ -450,12 +452,15 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "pygments"
-version = "2.12.0"
+version = "2.13.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[package.extras]
+plugins = ["importlib-metadata"]
+
 [[package]]
 name = "pyparam"
 version = "0.5.3"
@@ -490,14 +495,13 @@ python-versions = "*"
 
 [[package]]
 name = "pytest"
-version = "7.1.2"
+version = "7.1.3"
 description = "pytest: simple powerful testing with Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.dependencies]
-atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
 attrs = ">=19.2.0"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 iniconfig = "*"
@@ -522,7 +526,7 @@ coverage = {version = ">=5.2.1", extras = ["toml"]}
 pytest = ">=4.6"
 
 [package.extras]
-testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
+testing = ["virtualenv", "pytest-xdist", "six", "process-tests", "hunter", "fields"]
 
 [[package]]
 name = "python-dateutil"
@@ -537,7 +541,7 @@ six = ">=1.5"
 
 [[package]]
 name = "python-simpleconf"
-version = "0.5.6"
+version = "0.5.7"
 description = "Simple configuration management with python."
 category = "main"
 optional = false
@@ -570,7 +574,7 @@ unidecode = ["Unidecode (>=1.1.1)"]
 
 [[package]]
 name = "pytz"
-version = "2022.1"
+version = "2022.2.1"
 description = "World timezone definitions, modern and historical"
 category = "main"
 optional = false
@@ -578,7 +582,7 @@ python-versions = "*"
 
 [[package]]
 name = "rich"
-version = "12.4.4"
+version = "12.5.1"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 category = "main"
 optional = false
@@ -613,16 +617,15 @@ numpy = ">=1.16.5"
 
 [[package]]
 name = "setuptools-scm"
-version = "7.0.2"
+version = "6.4.2"
 description = "the blessed package to manage your versions by scm tags"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.6"
 
 [package.dependencies]
 packaging = ">=20.0"
 tomli = ">=1.0.0"
-typing-extensions = "*"
 
 [package.extras]
 test = ["pytest (>=6.2)", "virtualenv (>20)"]
@@ -682,7 +685,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "typing-extensions"
-version = "4.2.0"
+version = "4.3.0"
 description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "main"
 optional = false
@@ -690,518 +693,77 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "varname"
-version = "0.8.3"
+version = "0.8.2"
 description = "Dark magics about variable names in python."
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=3.6,<4.0"
 
 [package.dependencies]
 asttokens = ">=2.0.0,<3.0.0"
-executing = ">=0.8.3,<0.9.0"
+executing = "*"
 pure_eval = "<1.0.0"
 
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8"
-content-hash = "0126fb1cd90e9f3fc2ab4d141ccd842e4c51b9bd62f960e10980b3baab25f8a4"
+content-hash = "2acdb28d9f776b159567b259d264d22e317d00daa1afbcc14836ca33a6eee618"
 
 [metadata.files]
-asttokens = [
-    {file = "asttokens-2.0.5-py2.py3-none-any.whl", hash = "sha256:0844691e88552595a6f4a4281a9f7f79b8dd45ca4ccea82e5e05b4bbdb76705c"},
-    {file = "asttokens-2.0.5.tar.gz", hash = "sha256:9a54c114f02c7a9480d56550932546a3f1fe71d8a02f1bc7ccd0ee3ee35cf4d5"},
-]
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-    {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
-]
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+attrs = []
+click = []
+cmdy = []
+colorama = []
+coloredlogs = []
+commonmark = []
+coverage = []
+curio = []
+cycler = []
+cyvcf2 = []
+datar = []
+descartes = []
+diot = []
+executing = []
+fonttools = []
+humanfriendly = []
+inflection = []
+iniconfig = []
+kiwisolver = []
+lark-parser = []
+matplotlib = []
+mizani = []
+numpy = []
+packaging = []
+palettable = []
+pandas = []
+patsy = []
+pdtypes = []
+pillow = []
+pipda = []
+plotnine = []
+plotnine-prism = []
+pluggy = []
+pure-eval = []
+py = []
+pygments = []
+pyparam = []
+pyparsing = []
+pyreadline3 = []
+pytest = []
+pytest-cov = []
+python-dateutil = []
+python-simpleconf = []
+python-slugify = []
+pytz = []
+rich = []
+rtoml = []
+scipy = []
+setuptools-scm = []
+six = []
+statsmodels = []
+text-unidecode = []
+toml = []
+tomli = []
+typing-extensions = []
+varname = []
diff --git a/pyproject.toml b/pyproject.toml
index 797ace7..1e3b0bd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.masonry.api"
 
 [tool.poetry]
 name = "vcfstats"
-version = "0.4.1"
+version = "0.4.2"
 description = "Powerful statistics for VCF files"
 authors = [ "pwwang <pwwang@pwwang.com>",]
 license = "MIT"
@@ -16,13 +16,13 @@ include = ["vcfstats/args.toml"]
 [tool.poetry.dependencies]
 python = "^3.8"
 cyvcf2 = "0.*"
-pyparam = "^0.5"
+pyparam = "^0.5.1"
 rich = "^12"
 lark-parser = "^0.12"
 plotnine = "^0.8"
 plotnine-prism = "^0.0"
 python-slugify = "^6"
-datar = "^0.8"
+datar = "^0.9"
 py = "^1.10"
 # https://github.com/brentp/cyvcf2/issues/181
 numpy = "^1.22"
diff --git a/setup.py b/setup.py
deleted file mode 120000
index 7573be2..0000000
--- a/setup.py
+++ /dev/null
@@ -1 +0,0 @@
-dist/vcfstats-0.3.0/setup.py
\ No newline at end of file
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..8c4baa0
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,14 @@
+# -*- coding: utf-8 -*-
+"""
+This will not be included in the distribution.
+The distribution is managed by poetry
+This file is kept only for
+1. Github to index the dependents
+2. pip install -e .
+Do NOT use this to install this package, unless you handled the dependencies
+by your self:
+pip install git+https://...
+"""
+from setuptools import setup
+
+setup(name="vcfstats")
diff --git a/vcfstats/__init__.py b/vcfstats/__init__.py
index ebb4eda..aae7d81 100644
--- a/vcfstats/__init__.py
+++ b/vcfstats/__init__.py
@@ -3,4 +3,4 @@
 
 from . import macros
 
-__version__ = "0.4.1"
+__version__ = "0.4.2"
diff --git a/vcfstats/args.toml b/vcfstats/args.toml
index 665bd9a..fca9bc5 100644
--- a/vcfstats/args.toml
+++ b/vcfstats/args.toml
@@ -52,7 +52,7 @@ aliases = ['f']
 required = true
 type = 'list'
 desc = '''The formulas for plotting in format of `Y ~ X`,
-where `Y` and `X` should be either an entry or an aggregation.
+where `Y` and `X` should be either an entry or an aggregation. Optional when --config is given.
 '''
 
 [params.macro]
@@ -62,7 +62,7 @@ desc = 'A user-defined macro file.'
 [params.title]
 required = true
 type = 'list'
-desc = 'The title of each figure, will be used to name the output files as well.'
+desc = 'The title of each figure, will be used to name the output files as well. Optional when --config is given.'
 
 [params.ggs]
 default = []
diff --git a/vcfstats/cli.py b/vcfstats/cli.py
index abbed6b..715269b 100644
--- a/vcfstats/cli.py
+++ b/vcfstats/cli.py
@@ -61,7 +61,8 @@ def combine_regions(regions, regfile):
     """Combine all the regions.
     Users have to make sure there is no overlapping between regions"""
     logger.info(
-        "Combining regions, remind that regions should not be overlapping ..."
+        "Combining regions, be reminded that regions should "
+        "NOT be overlapping ..."
     )
     # make sure regions have no overlaps
     ret = regions[:] if regions else []
@@ -157,6 +158,10 @@ def load_config(config, opts):
     else:
         default_devpars = opts["devpars"]
         opts["devpars"] = [opts["devpars"]] * len_fml
+
+    if isinstance(default_devpars, Namespace):
+        default_devpars = default_devpars._to_dict()
+
     for instance in ones:
         if "formula" not in instance:
             raise ValueError(
@@ -186,15 +191,32 @@ def main():
             load_macrofile(sys.argv[sys.argv.index("--macro") + 1])
         list_macros()
 
-    opts = params.parse()
+    opts = params.parse(ignore_errors=True)
+    # title and formula can be optional if config file specified
+    if "formula" in opts or "title" in opts:
+        # raise other errors
+        opts = params.parse()
+    else:
+        opts["formula"] = []
+        opts["title"] = []
+
+    if "ggs" not in opts:
+        opts["ggs"] = []
+
     logger.setLevel(getattr(logging, opts["loglevel"].upper()))
+
     if opts["config"]:
         load_config(opts["config"], opts)
+
     if opts["macro"]:
         load_macrofile(opts["macro"])
+
     vcf, samples = get_vcf_by_regions(
+        # TODO: should write to a different file instead of appending to
+        # opts["Region"]
         opts["vcf"], combine_regions(opts["region"], opts["Region"])
     )
+
     ones = get_instances(opts, samples)
     logger.info("Start reading variants ...")
     with capture_c_msg("cyvcf2"):