diff --git a/galaxy/wrapper/plotCorrelation.xml b/galaxy/wrapper/plotCorrelation.xml
index 74ec67e0f0..f15c8b819c 100644
--- a/galaxy/wrapper/plotCorrelation.xml
+++ b/galaxy/wrapper/plotCorrelation.xml
@@ -114,7 +114,7 @@
             <param name="outFileFormat" value="png" />
             <param name="outFileCorMatrix" value="True" />
             <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />
-            <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="400" />
+            <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="2000" />
         </test>
         <test expect_num_outputs="1">
             <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
@@ -122,7 +122,7 @@
             <param name="whatToPlot" value="scatterplot" />
             <param name="removeOutliers" value="True" />
             <param name="plotTitle" value="Test Plot" />
-            <output name="outFileName" file="plotCorrelation_result2.png" ftype="png" compare="sim_size" delta="300" />
+            <output name="outFileName" file="plotCorrelation_result2.png" ftype="png" compare="sim_size" delta="2000" />
         </test>
     </tests>
     <help>
diff --git a/galaxy/wrapper/plotCoverage.xml b/galaxy/wrapper/plotCoverage.xml
index cf2d6f5382..ee925b9a16 100644
--- a/galaxy/wrapper/plotCoverage.xml
+++ b/galaxy/wrapper/plotCoverage.xml
@@ -121,7 +121,7 @@
             <param name="plotTitle" value="Test Title from Galaxy" />
             <param name="outRawCounts" value="True" />
             <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
-            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
+            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="9000" />
         </test>
         <test expect_num_outputs="2">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
@@ -132,7 +132,7 @@
             <param name="coverageThreshold" value="5" />
             <param name="coverageThreshold" value="10" />
             <param name="coverageThreshold" value="20" />
-            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
+            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="9000" />
             <output name="outFileCoverageMetrics" file="plotCoverage.metrics" ftype="tabular" />
         </test>
     </tests>
diff --git a/galaxy/wrapper/plotEnrichment.xml b/galaxy/wrapper/plotEnrichment.xml
index 955f737a78..265d150e5e 100644
--- a/galaxy/wrapper/plotEnrichment.xml
+++ b/galaxy/wrapper/plotEnrichment.xml
@@ -182,7 +182,7 @@
             <param name="showAdvancedOpt" value="yes" />
             <param name="minMappingQuality" value="0" />
             <param name="regionLabels" value="up down" />
-            <output name="outFileName" file="plotEnrichment_output.png" ftype="png" compare="sim_size" delta="1000" />
+            <output name="outFileName" file="plotEnrichment_output.png" ftype="png" compare="sim_size" delta="5500" />
             <output name="outFileRawCounts" file="plotEnrichment_output.txt" ftype="tabular" />
         </test>
     </tests>
diff --git a/galaxy/wrapper/plotHeatmap.xml b/galaxy/wrapper/plotHeatmap.xml
index c81f3a5e91..de2fe68368 100644
--- a/galaxy/wrapper/plotHeatmap.xml
+++ b/galaxy/wrapper/plotHeatmap.xml
@@ -265,13 +265,13 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
-            <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="4000" />
+            <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="10000" />
         </test>
         <test expect_num_outputs="1">
             <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="whatToShow" value="heatmap and colorbar" />
-            <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="4000" />
+            <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="11000" />
         </test>
     </tests>
     <help>
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-- pypi: https://files.pythonhosted.org/packages/f3/8d/5e5be3ced1d12966fefb5c4ea3b2a5b480afcea36406559442c6e31d4a48/multidict-6.7.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
-  name: multidict
-  version: 6.7.1
-  sha256: bfde23ef6ed9db7eaee6c37dcec08524cb43903c60b285b172b6c094711b3961
-  requires_dist:
-  - typing-extensions>=4.1.0 ; python_full_version < '3.11'
-  requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/f3/ab/a7653bce9a3b204be6a6931767a9e23595807bb84790ce6685e4d7e5bd08/nh3-0.3.6-cp38-abi3-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl
-  name: nh3
-  version: 0.3.6
-  sha256: a43ebd7543555c3ac1bc353023d0794e75cb76f6f18f19c32e95441496c0cc25
-  requires_python: '>=3.8'
-- pypi: https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl
-  name: webencodings
-  version: 0.5.1
-  sha256: a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78
-- pypi: https://files.pythonhosted.org/packages/f4/7e/a72dd26f3b0f4f2bf1dd8923c85f7ceb43172af56d63c7383eb62b332364/pygments-2.20.0-py3-none-any.whl
-  name: pygments
-  version: 2.20.0
-  sha256: 81a9e26dd42fd28a23a2d169d86d7ac03b46e2f8b59ed4698fb4785f946d0176
-  requires_dist:
-  - colorama>=0.4.6 ; extra == 'windows-terminal'
-  requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/f9/38/8b6fc7a8153cb49eb3a9a13acfa9eeb6cc476e37888781e593e6f02ac05e/spython-0.3.14-py3-none-any.whl
-  name: spython
-  version: 0.3.14
-  sha256: 72968583e498bc2a51f9acd0ed6bc0d7d1f7ccd491feaba5e2f7d944bc51da3a
-- pypi: https://files.pythonhosted.org/packages/fa/0a/11486d02add7b1384dff7374d124b1cfbb0ee864dcc9f6a2c0380638cf84/numpy-2.5.0-cp312-cp312-macosx_10_13_x86_64.whl
-  name: numpy
-  version: 2.5.0
-  sha256: 489780423903667933b4ed6197b6ec3b75ea5dd17d1d8f0f38d798feb6921561
-  requires_python: '>=3.12'
-- pypi: https://files.pythonhosted.org/packages/fb/76/641ae371508676492379f16e2fa48f4e2c11741bd63c48be4b12a6b09cba/aiosignal-1.4.0-py3-none-any.whl
-  name: aiosignal
-  version: 1.4.0
-  sha256: 053243f8b92b990551949e63930a839ff0cf0b0ebbe0597b0f3fb19e1a0fe82e
-  requires_dist:
-  - frozenlist>=1.1.0
-  - typing-extensions>=4.2 ; python_full_version < '3.13'
-  requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/fd/7b/122376b1fd3c62c1ed9dc80c931ace4844b3c55407b6fb2d199377c9736f/pydantic-2.13.4-py3-none-any.whl
-  name: pydantic
-  version: 2.13.4
-  sha256: 45a282cde31d808236fd7ea9d919b128653c8b38b393d1c4ab335c62924d9aba
-  requires_dist:
-  - annotated-types>=0.6.0
-  - pydantic-core==2.46.4
-  - typing-extensions>=4.14.1
-  - typing-inspection>=0.4.2
-  - email-validator>=2.0.0 ; extra == 'email'
-  - tzdata ; python_full_version >= '3.9' and sys_platform == 'win32' and extra == 'timezone'
-  requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/fd/99/757a48b4ace0097b63550597db28f58da0b91d89889f98b34b30f272c0bf/ct3-3.4.0.post5-cp314-cp314-macosx_11_0_arm64.whl
-  name: ct3
-  version: 3.4.0.post5
-  sha256: 9611a4052fd76df8bd8961be0f8d94150908f712f910fcf22b2ceddae8f1882a
-  requires_dist:
-  - markdown ; extra == 'filters'
-  - markdown ; extra == 'markdown'
-  requires_python: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*'
-- pypi: https://files.pythonhosted.org/packages/fd/e1/3542a9cb596cadd76fcef413f19c79216e002623158befe6daa03dbfa88c/contourpy-1.3.3-cp314-cp314-macosx_11_0_arm64.whl
-  name: contourpy
-  version: 1.3.3
-  sha256: cbedb772ed74ff5be440fa8eee9bd49f64f6e3fc09436d9c7d8f1c287b121d77
-  requires_dist:
-  - numpy>=1.25
-  - furo ; extra == 'docs'
-  - sphinx>=7.2 ; extra == 'docs'
-  - sphinx-copybutton ; extra == 'docs'
-  - bokeh ; extra == 'bokeh'
-  - selenium ; extra == 'bokeh'
-  - contourpy[bokeh,docs] ; extra == 'mypy'
-  - bokeh ; extra == 'mypy'
-  - docutils-stubs ; extra == 'mypy'
-  - mypy==1.17.0 ; extra == 'mypy'
-  - types-pillow ; extra == 'mypy'
-  - contourpy[test-no-images] ; extra == 'test'
-  - matplotlib ; extra == 'test'
-  - pillow ; extra == 'test'
-  - pytest ; extra == 'test-no-images'
-  - pytest-cov ; extra == 'test-no-images'
-  - pytest-rerunfailures ; extra == 'test-no-images'
-  - pytest-xdist ; extra == 'test-no-images'
-  - wurlitzer ; extra == 'test-no-images'
-  requires_python: '>=3.11'
-- pypi: https://files.pythonhosted.org/packages/fe/cf/18ef143a81610136d3da8193da9d80bfe1cb548a1e2d1c775f26b23d024a/multidict-6.7.1-cp312-cp312-macosx_10_13_x86_64.whl
-  name: multidict
-  version: 6.7.1
-  sha256: 3fccb473e87eaa1382689053e4a4618e7ba7b9b9b8d6adf2027ee474597128cd
-  requires_dist:
-  - typing-extensions>=4.1.0 ; python_full_version < '3.11'
-  requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/ff/9a/9afaade874b2fa6c752c36f1548f718b5b83af81ed9b76628329dab81c1b/rfc3986-2.0.0-py2.py3-none-any.whl
-  name: rfc3986
-  version: 2.0.0
-  sha256: 50b1502b60e289cb37883f3dfd34532b8873c7de9f49bb546641ce9cbd256ebd
-  requires_dist:
-  - idna ; extra == 'idna2008'
-  requires_python: '>=3.7'
diff --git a/pydeeptools/deeptools/computeGCBias.py b/pydeeptools/deeptools/computeGCBias.py
index f261a9fc14..65be21e036 100755
--- a/pydeeptools/deeptools/computeGCBias.py
+++ b/pydeeptools/deeptools/computeGCBias.py
@@ -78,7 +78,7 @@ def getRequiredArgs():
                           'the observed and expected read frequencies per %%GC-'
                           'content. This file is needed to run the '
                           'correctGCBias tool. This is a text file.',
-                          type=argparse.FileType('w'),
+                          type=parserCommon.writableFile,
                           metavar='FILE',
                           required=True)
 
@@ -102,7 +102,7 @@ def getRequiredArgs():
                           help='BED file containing genomic regions for which '
                           'extra sampling is required because they are '
                           'underrepresented in the genome.',
-                          type=argparse.FileType('r'),
+                          type=parserCommon.readableFile,
                           metavar='BED file')
 
     plot = parser.add_argument_group('Diagnostic plot options')
@@ -640,11 +640,7 @@ def plotGCbias(file_name, frequencies, reads_per_gc, region_size, image_format=N
 def main(args=None):
     args = parse_arguments().parse_args(args)
 
-    if args.extraSampling:
-        extra_sampling_file = args.extraSampling.name
-        args.extraSampling.close()
-    else:
-        extra_sampling_file = None
+    extra_sampling_file = args.extraSampling if args.extraSampling else None
 
     global global_vars
     global_vars = {}
@@ -712,7 +708,7 @@ def main(args=None):
                              verbose=args.verbose,
                              region=args.region)
 
-    np.savetxt(args.GCbiasFrequenciesFile.name, data)
+    np.savetxt(args.GCbiasFrequenciesFile, data)
 
     if args.biasPlot:
         reads_per_gc = countReadsPerGC(args.regionSize,
diff --git a/pydeeptools/deeptools/computeMatrix.py b/pydeeptools/deeptools/computeMatrix.py
index 79e13dea9a..5ff67f831f 100644
--- a/pydeeptools/deeptools/computeMatrix.py
+++ b/pydeeptools/deeptools/computeMatrix.py
@@ -123,7 +123,7 @@ def computeMatrixOutputArgs(args=None):
                         'generate other heatmaps keeping the sorting of the '
                         'first heatmap. Example: Heatmap1sortedRegions.bed',
                         metavar='BED file',
-                        type=argparse.FileType('w'))
+                        type=writableFile)
     return parser
 
 
@@ -425,4 +425,5 @@ def main(args=None):
         hm.save_matrix_values(args.outFileNameMatrix)
 
     if args.outFileSortedRegions:
-        hm.save_BED(args.outFileSortedRegions)
+        with open(args.outFileSortedRegions, 'w') as f:
+            hm.save_BED(f)
diff --git a/pydeeptools/deeptools/computeMatrix2.py b/pydeeptools/deeptools/computeMatrix2.py
index a0853e3382..bbdd074b76 100644
--- a/pydeeptools/deeptools/computeMatrix2.py
+++ b/pydeeptools/deeptools/computeMatrix2.py
@@ -136,7 +136,7 @@ def computeMatrixOutputArgs(args=None):
         "generate other heatmaps keeping the sorting of the "
         "first heatmap. Example: Heatmap1sortedRegions.bed",
         metavar="BED file",
-        type=argparse.FileType("w"),
+        type=writableFile,
     )
     return parser
 
@@ -462,12 +462,7 @@ def main(args=None):
     args = process_args(args)
     signal.signal(signal.SIGINT, signal.SIG_DFL)
 
-    # Handle outFileSortedRegions: argparse.FileType("w") opens a file handle,
-    # but Rust handles file writing itself, so pass the filename and close the handle.
-    sorted_regions_file = None
-    if args.outFileSortedRegions is not None:
-        sorted_regions_file = args.outFileSortedRegions.name
-        args.outFileSortedRegions.close()
+    sorted_regions_file = args.outFileSortedRegions
 
     r_computematrix(
         args.command,
diff --git a/pydeeptools/deeptools/correctGCBias.py b/pydeeptools/deeptools/correctGCBias.py
index 1154b93688..99c725c4fc 100755
--- a/pydeeptools/deeptools/correctGCBias.py
+++ b/pydeeptools/deeptools/correctGCBias.py
@@ -91,7 +91,7 @@ def getRequiredArgs():
                           'computeGCBias containing '
                           'the observed and expected read frequencies per GC-'
                           'content.',
-                          type=argparse.FileType('r'),
+                          type=parserCommon.readableFile,
                           metavar='FILE',
                           required=True)
 
@@ -102,7 +102,7 @@ def getRequiredArgs():
                         'are ".bam", ".bw" for a bigWig file, ".bg" for a '
                         'bedGraph file.',
                         metavar='FILE',
-                        type=argparse.FileType('w'),
+                        type=parserCommon.writableFile,
                         required=True)
 
     # define the optional arguments
@@ -553,7 +553,7 @@ def main(args=None):
     args = process_args(args)
     global F_gc, N_gc, R_gc
 
-    data = np.loadtxt(args.GCbiasFrequenciesFile.name)
+    data = np.loadtxt(args.GCbiasFrequenciesFile)
 
     F_gc = data[:, 0]
     N_gc = data[:, 1]
@@ -623,7 +623,7 @@ def main(args=None):
 
     pool = multiprocessing.Pool(args.numberOfProcessors)
 
-    if args.correctedFile.name.endswith('bam'):
+    if args.correctedFile.endswith('bam'):
         if len(mp_args) > 1 and args.numberOfProcessors > 1:
             print(("using {} processors for {} "
                    "number of tasks".format(args.numberOfProcessors,
@@ -635,12 +635,12 @@ def main(args=None):
             res = list(map(writeCorrectedSam_wrapper, mp_args))
 
         if len(res) == 1:
-            command = "cp {} {}".format(res[0], args.correctedFile.name)
+            command = "cp {} {}".format(res[0], args.correctedFile)
             run_shell_command(command)
         else:
             print("concatenating (sorted) intermediate BAMs")
             header = pysam.Samfile(res[0])
-            of = pysam.Samfile(args.correctedFile.name, "wb", template=header)
+            of = pysam.Samfile(args.correctedFile, "wb", template=header)
             header.close()
             for f in res:
                 f = pysam.Samfile(f)
@@ -650,13 +650,13 @@ def main(args=None):
             of.close()
 
         print("indexing BAM")
-        pysam.index(args.correctedFile.name)
+        pysam.index(args.correctedFile)
 
         for tempFileName in res:
             os.remove(tempFileName)
 
-    if args.correctedFile.name.endswith('bg') or \
-            args.correctedFile.name.endswith('bw'):
+    if args.correctedFile.endswith('bg') or \
+            args.correctedFile.endswith('bw'):
 
         if len(mp_args) > 1 and args.numberOfProcessors > 1:
 
@@ -664,8 +664,7 @@ def main(args=None):
         else:
             res = list(map(writeCorrected_wrapper, mp_args))
 
-        oname = args.correctedFile.name
-        args.correctedFile.close()
+        oname = args.correctedFile
         if oname.endswith('bg'):
             f = open(oname, 'wb')
             for tempFileName in res:
diff --git a/pydeeptools/deeptools/correlation.py b/pydeeptools/deeptools/correlation.py
index 13ac642c82..cd7a35acb6 100644
--- a/pydeeptools/deeptools/correlation.py
+++ b/pydeeptools/deeptools/correlation.py
@@ -230,10 +230,13 @@ def compute_correlation(self):
 
     def plot_correlation(self, plot_filename, plot_title='', vmax=None,
                          vmin=None, colormap='jet', image_format=None,
-                         plot_numbers=False, plotWidth=11, plotHeight=9.5):
+                         plot_numbers=False, plotWidth=11, plotHeight=9.5, ggplot=False):
         """
         plots a correlation using a symmetric heatmap
         """
+        if ggplot:
+            plt.style.use('ggplot')
+        
         num_rows = len(self.labels)
         corr_matrix = self.compute_correlation()
         # set a font size according to figure length
diff --git a/pydeeptools/deeptools/matplotlib_defaults.py b/pydeeptools/deeptools/matplotlib_defaults.py
index 4b62527352..8c69a2383d 100644
--- a/pydeeptools/deeptools/matplotlib_defaults.py
+++ b/pydeeptools/deeptools/matplotlib_defaults.py
@@ -1,22 +1,71 @@
 import matplotlib
 
-# Backend should be set before importing pyplot
+# Backend must be set before importing pyplot
 matplotlib.use("Agg")
 
-# Central matplotlib configuration
 matplotlib.rcParams.update({
 
+    # --------------------------------------------------
     # Output compatibility
+    # --------------------------------------------------
     "pdf.fonttype": 42,
     "ps.fonttype": 42,
     "svg.fonttype": "none",
 
+    # --------------------------------------------------
     # Fonts
+    # --------------------------------------------------
+    "font.family": "sans-serif",
+    "font.sans-serif": ["DejaVu Sans"],
     "font.size": 8.0,
 
+    # Stabilize FreeType rendering
+    "text.hinting": "none",
+
+    # --------------------------------------------------
     # Figure defaults
+    # --------------------------------------------------
     "figure.dpi": 100,
-    "savefig.dpi": 200,
-})
+    "savefig.dpi": 100,
+    "figure.figsize": [6.4, 4.8],
+
+    "figure.facecolor": "white",
+    "axes.facecolor": "white",
+    "savefig.facecolor": "white",
+
+    # Disable automatic layout changes
+    "figure.autolayout": False,
+    "figure.constrained_layout.use": False,
+
+    # --------------------------------------------------
+    # Axes / labels
+    # --------------------------------------------------
+    "axes.titlesize": 8.0,
+    "axes.labelsize": 8.0,
+
+    "xtick.labelsize": 8.0,
+    "ytick.labelsize": 8.0,
+
+    "axes.autolimit_mode": "data",
+    "axes.xmargin": 0,
+    "axes.ymargin": 0,
+
+    # --------------------------------------------------
+    # Lines and paths
+    # --------------------------------------------------
+    "lines.linewidth": 1.5,
+
+    "path.simplify": False,
+    "path.simplify_threshold": 0.0,
 
+    # --------------------------------------------------
+    # Images
+    # --------------------------------------------------
+    "image.interpolation": "nearest",
+    "image.resample": False,
 
+    # --------------------------------------------------
+    # Legend
+    # --------------------------------------------------
+    "legend.fontsize": 8.0,
+})
\ No newline at end of file
diff --git a/pydeeptools/deeptools/parserCommon.py b/pydeeptools/deeptools/parserCommon.py
index a65f68667b..70b4aff219 100755
--- a/pydeeptools/deeptools/parserCommon.py
+++ b/pydeeptools/deeptools/parserCommon.py
@@ -414,6 +414,18 @@ def writableFile(string):
     return string
 
 
+def readableFile(string):
+    """
+    Simple function that tests if a given path is readable
+    """
+    try:
+        open(string, 'r').close()
+    except OSError as e:
+        msg = "{} file can't be opened for reading: {}".format(string, e)
+        raise argparse.ArgumentTypeError(msg)
+    return string
+
+
 """
 Arguments used by heatmapper and profiler
 """
@@ -424,7 +436,7 @@ def heatmapperMatrixArgs(args=None):
     required = parser.add_argument_group('Required arguments')
     required.add_argument('--matrixFile', '-m',
                           help='Matrix file from the computeMatrix tool.',
-                          type=argparse.FileType('r'),
+                          type=readableFile,
                           )
 
     required.add_argument('--outFileName', '-out', '-o',
@@ -451,7 +463,7 @@ def heatmapperOutputArgs(args=None,
         'generate other heatmaps while keeping the sorting of the '
         'first heatmap. Example: Heatmap1sortedRegions.bed',
         metavar='FILE',
-        type=argparse.FileType('w'))
+        type=writableFile)
 
     if mode == 'heatmap':
         output.add_argument('--outFileNameMatrix',
diff --git a/pydeeptools/deeptools/plotCorrelation.py b/pydeeptools/deeptools/plotCorrelation.py
index 1aa7118e9a..e6c23ee8bf 100644
--- a/pydeeptools/deeptools/plotCorrelation.py
+++ b/pydeeptools/deeptools/plotCorrelation.py
@@ -92,6 +92,10 @@ def plot_correlation_args():
                           'the generated image. Leave blank for no title. (Default: %(default)s)',
                           default='')
 
+    optional.add_argument('--ggplot',
+                          help='Use ggplot theme for figures',
+                          action='store_true')
+    
     optional.add_argument('--plotFileFormat',
                           metavar='FILETYPE',
                           help='Image format type. If given, this option '
diff --git a/pydeeptools/deeptools/plotHeatmap.py b/pydeeptools/deeptools/plotHeatmap.py
index 55fe70f96e..6432f9356e 100755
--- a/pydeeptools/deeptools/plotHeatmap.py
+++ b/pydeeptools/deeptools/plotHeatmap.py
@@ -5,8 +5,8 @@
 import argparse
 from collections import OrderedDict
 import numpy as np
-import matplotlib
 from deeptools import matplotlib_defaults
+import matplotlib
 import matplotlib.pyplot as plt
 from matplotlib.font_manager import FontProperties
 import matplotlib.gridspec as gridspec
@@ -604,7 +604,7 @@ def plotMatrix(hm, outFileName,
         #  When no box is plotted the space between heatmaps is reduced
         fig.get_layout_engine().set(wspace=0.05, hspace=0.01, rect=(0.04, 0, 0.96, 0.85))
 
-    plt.savefig(outFileName, bbox_inches='tight', pad_inches=0.1, dpi=dpi, format=image_format)
+    plt.savefig(outFileName, dpi=dpi, format=image_format)
     plt.close()
 
 
@@ -647,9 +647,7 @@ def mergeSmallGroups(matrixDict):
 def main(args=None):
     args = process_args(args)
     hm = heatmapper.heatmapper()
-    matrix_file = args.matrixFile.name
-    args.matrixFile.close()
-    hm.read_matrix_file(matrix_file)
+    hm.read_matrix_file(args.matrixFile)
 
     if hm.parameters['min threshold'] is not None or hm.parameters['max threshold'] is not None:
         filterHeatmapValues(hm, hm.parameters['min threshold'], hm.parameters['max threshold'])
@@ -703,7 +701,8 @@ def main(args=None):
         hm.save_matrix(args.outFileNameMatrix)
 
     if args.outFileSortedRegions:
-        hm.save_BED(args.outFileSortedRegions)
+        with open(args.outFileSortedRegions, 'w') as f:
+            hm.save_BED(f)
 
     if not args.label_rotation:
         label_rotation=45.0
diff --git a/pydeeptools/deeptools/plotProfile.py b/pydeeptools/deeptools/plotProfile.py
index 0371208c4e..0ac37fb81d 100755
--- a/pydeeptools/deeptools/plotProfile.py
+++ b/pydeeptools/deeptools/plotProfile.py
@@ -597,9 +597,7 @@ def plot_profile(self):
 def main(args=None):
     args = process_args(args)
     hm = heatmapper.heatmapper()
-    matrix_file = args.matrixFile.name
-    args.matrixFile.close()
-    hm.read_matrix_file(matrix_file)
+    hm.read_matrix_file(args.matrixFile)
 
     if hm.parameters['min threshold'] is not None or hm.parameters['max threshold'] is not None:
         filterHeatmapValues(hm, hm.parameters['min threshold'], hm.parameters['max threshold'])
@@ -630,7 +628,8 @@ def main(args=None):
                                  averagetype=args.averageType)
 
     if args.outFileSortedRegions:
-        hm.save_BED(args.outFileSortedRegions)
+        with open(args.outFileSortedRegions, 'w') as f:
+            hm.save_BED(f)
 
     prof = Profile(hm, args.outFileName,
                    plot_title=args.plotTitle,
diff --git a/pydeeptools/deeptools/test/conftest.py b/pydeeptools/deeptools/test/conftest.py
new file mode 100644
index 0000000000..a9c7f43c7f
--- /dev/null
+++ b/pydeeptools/deeptools/test/conftest.py
@@ -0,0 +1,10 @@
+import matplotlib
+import matplotlib.pyplot as plt
+import pytest
+
+
+@pytest.fixture(autouse=True)
+def _isolate_matplotlib_rcparams():
+    with matplotlib.rc_context():
+        yield
+    plt.close("all")
diff --git a/pydeeptools/deeptools/test/test_bamPEFragmentSize.py b/pydeeptools/deeptools/test/test_bamPEFragmentSize.py
index 011dc30d5a..5423f0edc0 100644
--- a/pydeeptools/deeptools/test/test_bamPEFragmentSize.py
+++ b/pydeeptools/deeptools/test/test_bamPEFragmentSize.py
@@ -1,52 +1,148 @@
 import os.path
-from os import unlink
 import tempfile
 
 from matplotlib.testing.compare import compare_images
 
 import deeptools.bamPEFragmentSize
 
+
 ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data"
 
+# Headroom for anti-aliasing/text-hinting drift between matplotlib patch
+# versions (e.g. 3.10.x vs 3.11.x render identical plots with slightly
+# different sub-pixel edges); see matplotlib_defaults.py.
+tolerance = 15
 
-def test_bamPEFragmentSize_histogram():
+
+def run_bamPEFragmentSize_histogram(extra_args=None):
     """
-    Test histogram plot for bamPEFragmentSize
+    Run bamPEFragmentSize histogram and return generated png file.
     """
-    _, outfile = tempfile.mkstemp(suffix=".png")
-    args = "--bamfiles {}/bowtie2_test1.bam --samplesLabel bowtie2_test1.bam --plotFileFormat png --plotTitle Test-Plot --histogram {}".format(
-        ROOT, outfile
+
+    fd, outfile = tempfile.mkstemp(suffix=".png")
+    os.close(fd)
+
+    args = (
+        f"--bamfiles {ROOT}/bowtie2_test1.bam "
+        f"--samplesLabel bowtie2_test1.bam "
+        f"--plotFileFormat png "
+        f"--plotTitle Test-Plot "
+        f"--histogram {outfile}"
     ).split()
+
+    if extra_args:
+        args.extend(extra_args)
+
     deeptools.bamPEFragmentSize.main(args)
 
-    res = compare_images(ROOT + "/bamPEFragmentSize_histogram_result1.png", outfile, 10)
-    assert res is None, res
+    return outfile
+
+
+def cleanup(*files):
+    """
+    Remove temporary files.
+    """
+    for f in files:
+        if f and os.path.exists(f):
+            os.remove(f)
+
+
+def test_bamPEFragmentSize_histogram():
+    """
+    Test histogram plot for bamPEFragmentSize.
+    """
+
+    outfile = run_bamPEFragmentSize_histogram()
+
+    try:
+        res = compare_images(
+            ROOT + "/bamPEFragmentSize_histogram_result1.png",
+            outfile,
+            tolerance
+        )
+
+        assert res is None, res
+
+    finally:
+        cleanup(outfile)
+
+
+def test_bamPEFragmentSize_histogram_ggplot():
+    """
+    Test histogram plot for bamPEFragmentSize using --ggplot.
+    """
+
+    outfile = run_bamPEFragmentSize_histogram(
+        ["--ggplot"]
+    )
+
+    try:
+        res = compare_images(
+            ROOT + "/bamPEFragmentSize_histogram_ggplot.png",
+            outfile,
+            tolerance
+        )
+
+        assert res is None, res
+
+    finally:
+        cleanup(outfile)
 
 
 def test_bamPEFragmentSize_fr_sizes():
     """
-    Test fragment length information for bamPEFragmentSize
+    Test fragment length information for bamPEFragmentSize.
     """
-    _, out_lengths = tempfile.mkstemp(suffix=".txt")
-    _, out_metrics = tempfile.mkstemp(suffix=".txt")
+
+    fd, out_lengths = tempfile.mkstemp(suffix=".txt")
+    os.close(fd)
+
+    fd, out_metrics = tempfile.mkstemp(suffix=".txt")
+    os.close(fd)
+
     args = (
-        "--bamfiles {}/bowtie2_test1.bam --outRawFragmentLengths {} --table {}".format(
-            ROOT, out_lengths, out_metrics
-        ).split()
-    )
+        f"--bamfiles {ROOT}/bowtie2_test1.bam "
+        f"--outRawFragmentLengths {out_lengths} "
+        f"--table {out_metrics}"
+    ).split()
+
     deeptools.bamPEFragmentSize.main(args)
 
-    l = open(out_lengths, "r")
-    l_resp = l.readlines()
-    l.close()
-    l_expected = ["241\t1", "242\t1", "251\t1"]
-    matches = [
-        expected for expected in l_expected if any(expected in resp for resp in l_resp)
-    ]
-    assert matches == l_expected
-
-    m = open(out_metrics, "r")
-    m_resp = m.readlines()[1]
-    m.close()
-    m_expected = "3\t241.0\t241.5\t244.66666666666666\t242.0\t246.5\t251.0\t4.496912521077347\t1.0\t241.2\t241.4\t241.6\t241.8\t243.8\t245.6\t247.4\t249.2\t250.82\t3\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\t0.0\t0.0\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\n"
-    assert m_expected in f"{m_resp}"
+    try:
+
+        with open(out_lengths, "r") as l:
+            l_resp = l.readlines()
+
+        l_expected = [
+            "241\t1",
+            "242\t1",
+            "251\t1"
+        ]
+
+        matches = [
+            expected
+            for expected in l_expected
+            if any(expected in resp for resp in l_resp)
+        ]
+
+        assert matches == l_expected
+
+
+        with open(out_metrics, "r") as m:
+            m_resp = m.readlines()[1]
+
+
+        m_expected = (
+            "3\t241.0\t241.5\t244.66666666666666\t242.0\t246.5\t251.0\t"
+            "4.496912521077347\t1.0\t241.2\t241.4\t241.6\t241.8\t243.8\t245.6\t"
+            "247.4\t249.2\t250.82\t3\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\t"
+            "0.0\t0.0\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\n"
+        )
+
+        assert m_expected in m_resp
+
+    finally:
+        cleanup(
+            out_lengths,
+            out_metrics
+        )
\ No newline at end of file
diff --git a/pydeeptools/deeptools/test/test_data/bamPEFragmentSize_histogram_ggplot.png b/pydeeptools/deeptools/test/test_data/bamPEFragmentSize_histogram_ggplot.png
new file mode 100644
index 0000000000..2e3a383eab
Binary files /dev/null and b/pydeeptools/deeptools/test/test_data/bamPEFragmentSize_histogram_ggplot.png differ
diff --git a/pydeeptools/deeptools/test/test_data/bamPEFragmentSize_histogram_result1.png b/pydeeptools/deeptools/test/test_data/bamPEFragmentSize_histogram_result1.png
index 1547aefd23..78d04cae63 100644
Binary files a/pydeeptools/deeptools/test/test_data/bamPEFragmentSize_histogram_result1.png and b/pydeeptools/deeptools/test/test_data/bamPEFragmentSize_histogram_result1.png differ
diff --git a/pydeeptools/deeptools/test/test_data/plotCorrelation_result1.png b/pydeeptools/deeptools/test/test_data/plotCorrelation_result1.png
index 85d1fc134c..6c69198124 100644
Binary files a/pydeeptools/deeptools/test/test_data/plotCorrelation_result1.png and b/pydeeptools/deeptools/test/test_data/plotCorrelation_result1.png differ
diff --git a/pydeeptools/deeptools/test/test_data/plotCorrelation_result1_ggplot.png b/pydeeptools/deeptools/test/test_data/plotCorrelation_result1_ggplot.png
new file mode 100644
index 0000000000..6c69198124
Binary files /dev/null and b/pydeeptools/deeptools/test/test_data/plotCorrelation_result1_ggplot.png differ
diff --git a/pydeeptools/deeptools/test/test_data/plotCorrelation_result2.png b/pydeeptools/deeptools/test/test_data/plotCorrelation_result2.png
index 343ae41ba4..d46e8b0296 100644
Binary files a/pydeeptools/deeptools/test/test_data/plotCorrelation_result2.png and b/pydeeptools/deeptools/test/test_data/plotCorrelation_result2.png differ
diff --git a/pydeeptools/deeptools/test/test_data/plotCorrelation_result2_ggplot.png b/pydeeptools/deeptools/test/test_data/plotCorrelation_result2_ggplot.png
new file mode 100644
index 0000000000..d46e8b0296
Binary files /dev/null and b/pydeeptools/deeptools/test/test_data/plotCorrelation_result2_ggplot.png differ
diff --git a/pydeeptools/deeptools/test/test_matplotversion.py b/pydeeptools/deeptools/test/test_matplotversion.py
new file mode 100644
index 0000000000..8f7942a98d
--- /dev/null
+++ b/pydeeptools/deeptools/test/test_matplotversion.py
@@ -0,0 +1,78 @@
+from pathlib import Path
+import sys
+import tomllib
+import matplotlib
+import deeptools
+
+
+def find_pyproject():
+
+    current_path = Path(__file__).resolve()
+
+    for parent in current_path.parents:
+        pyproject = parent / "pyproject.toml"
+
+        if pyproject.exists():
+            return pyproject
+
+    raise FileNotFoundError(
+        "pyproject.toml not found"
+    )
+
+
+def get_matplotlib_requirement():
+
+    pyproject = find_pyproject()
+
+    with open(pyproject, "rb") as f:
+        config = tomllib.load(f)
+
+    dependencies = config["project"]["dependencies"]
+
+    for dependency in dependencies:
+        if dependency.startswith("matplotlib"):
+            return dependency
+
+    raise RuntimeError(
+        "matplotlib dependency not found in pyproject.toml"
+    )
+
+
+def test_matplotlib_version():
+
+    print("\nPython executable:")
+    print(sys.executable)
+
+    print("\nMatplotlib version:")
+    print(matplotlib.__version__)
+
+    print("\nMatplotlib path:")
+    print(matplotlib.__file__)
+
+    print("\ndeepTools path:")
+    print(deeptools.__file__)
+
+    requirement = get_matplotlib_requirement()
+
+    print("\nMatplotlib requirement from pyproject.toml:")
+    print(requirement)
+
+    # Example: "matplotlib >= 3.9"
+    min_version = (
+        requirement
+        .split(">=")[1]
+        .strip()
+    )
+
+    required = tuple(
+        map(int, min_version.split(".")[:2])
+    )
+
+    installed = tuple(
+        map(int, matplotlib.__version__.split(".")[:2])
+    )
+
+    assert installed >= required, (
+        f"Installed matplotlib {matplotlib.__version__} "
+        f"does not satisfy {requirement}"
+    )
\ No newline at end of file
diff --git a/pydeeptools/deeptools/test/test_plotCoverage.py b/pydeeptools/deeptools/test/test_plotCoverage.py
index 81eb16bc95..03b7d62831 100644
--- a/pydeeptools/deeptools/test/test_plotCoverage.py
+++ b/pydeeptools/deeptools/test/test_plotCoverage.py
@@ -2,27 +2,95 @@
 import filecmp
 from matplotlib.testing.compare import compare_images
 from tempfile import NamedTemporaryFile
+
 import deeptools.plotCoverage
 import deeptools.utilities
 
+
 __author__ = 'Bjoern'
 
+
 TEST_DATA = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
 ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_plotCoverage/"
 
-tolerance = 13  # default matplotlib pixed difference tolerance
+tolerance = 13
+
+
+def run_plotCoverage(extra_args=None):
+    """Run plotCoverage and return generated plot and raw count files."""
+
+    plotfile = NamedTemporaryFile(
+        suffix='.png',
+        prefix='deeptools_testfile_',
+        delete=False
+    )
+
+    txtfile = NamedTemporaryFile(
+        suffix='.tab',
+        prefix='deeptools_testfile_',
+        delete=False
+    )
+
+    args = (
+        f"--bamfiles {TEST_DATA}test1.bam "
+        f"{TEST_DATA}test2.bam "
+        f"--plotFile {plotfile.name} "
+        f"--plotFileFormat png "
+        f"--outRawCounts {txtfile.name}"
+    ).split()
+
+    if extra_args:
+        args.extend(extra_args)
+
+    deeptools.plotCoverage.main(args)
+
+    return plotfile.name, txtfile.name
+
+
+def cleanup(*files):
+    for f in files:
+        if os.path.exists(f):
+            os.remove(f)
 
 
 def test_plotCoverage_default():
-    plotfile = NamedTemporaryFile(suffix='.png', prefix='deeptools_testfile_', delete=False)
-    txtfile = NamedTemporaryFile(suffix='.tab', prefix='deeptools_testfile_', delete=False)
+    """Test default plotCoverage output and raw counts."""
+
+    plotfile, txtfile = run_plotCoverage()
+
+    try:
+        assert filecmp.cmp(
+            os.path.join(ROOT, "outRawCounts_default.tabular"),
+            txtfile
+        ) is True
 
-    for fmat in ["bam", "cram"]:
-        args = "--bamfiles {0}test1.{3} {0}test2.{3} --plotFile {1}" \
-               " --plotFileFormat png --outRawCounts {2}".format(TEST_DATA, plotfile.name, txtfile.name, fmat).split()
-        deeptools.plotCoverage.main(args)
-        if fmat == "bam":
-            assert filecmp.cmp(os.path.join(ROOT, 'outRawCounts_default.tabular'), txtfile.name) is True
+        res = compare_images(
+            os.path.join(ROOT, "plotCoverage_default.png"),
+            plotfile,
+            tolerance
+        )
 
-        res = compare_images(ROOT + 'plotCoverage_default.png', plotfile.name, tolerance)
         assert res is None, res
+
+    finally:
+        print(plotfile, txtfile)
+
+
+def test_plotCoverage_ggplot():
+    """Test plotCoverage output with --ggplot."""
+
+    plotfile, txtfile = run_plotCoverage(
+        ["--ggplot"]
+    )
+
+    try:
+        res = compare_images(
+            os.path.join(ROOT, "plotCoverage_ggplot.png"),
+            plotfile,
+            tolerance
+        )
+
+        assert res is None, res
+
+    finally:
+        print(plotfile, txtfile)
\ No newline at end of file
diff --git a/pydeeptools/deeptools/test/test_plotCoverage/plotCoverage_default.png b/pydeeptools/deeptools/test/test_plotCoverage/plotCoverage_default.png
index 8465db2e04..82949d8126 100644
Binary files a/pydeeptools/deeptools/test/test_plotCoverage/plotCoverage_default.png and b/pydeeptools/deeptools/test/test_plotCoverage/plotCoverage_default.png differ
diff --git a/pydeeptools/deeptools/test/test_plotCoverage/plotCoverage_ggplot.png b/pydeeptools/deeptools/test/test_plotCoverage/plotCoverage_ggplot.png
new file mode 100644
index 0000000000..552b0bbf15
Binary files /dev/null and b/pydeeptools/deeptools/test/test_plotCoverage/plotCoverage_ggplot.png differ
diff --git a/pydeeptools/deeptools/test/test_plotEnrichment.py b/pydeeptools/deeptools/test/test_plotEnrichment.py
index 1f1fc814bc..6abaa8de04 100644
--- a/pydeeptools/deeptools/test/test_plotEnrichment.py
+++ b/pydeeptools/deeptools/test/test_plotEnrichment.py
@@ -2,28 +2,99 @@
 import filecmp
 from matplotlib.testing.compare import compare_images
 from tempfile import NamedTemporaryFile
+
 import deeptools.plotEnrichment
 import deeptools.utilities
 
+
 __author__ = 'Bjoern'
 
+
 TEST_DATA = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
 ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_plotEnrichment/"
 
-tolerance = 13  # default matplotlib pixed difference tolerance
+# Headroom for anti-aliasing/text-hinting drift between matplotlib patch
+# versions (e.g. 3.10.x vs 3.11.x render identical plots with slightly
+# different sub-pixel edges); see matplotlib_defaults.py.
+tolerance = 20
+
+
+def run_plotEnrichment(extra_args=None):
+    """Run plotEnrichment and return generated plot and count files."""
+
+    plotfile = NamedTemporaryFile(
+        suffix='.png',
+        prefix='deeptools_testfile_',
+        delete=False
+    )
+
+    txtfile = NamedTemporaryFile(
+        suffix='.tab',
+        prefix='deeptools_testfile_',
+        delete=False
+    )
+
+    args = (
+        f"--bamfiles {TEST_DATA}test1.bam "
+        f"{TEST_DATA}test2.bam "
+        f"--BED {TEST_DATA}test.gtf "
+        f"--plotFile {plotfile.name} "
+        f"--plotFileFormat png "
+        f"--outRawCounts {txtfile.name}"
+    ).split()
+
+    if extra_args:
+        args.extend(extra_args)
+
+    deeptools.plotEnrichment.main(args)
+
+    return plotfile.name, txtfile.name
+
+
+def cleanup(*files):
+    for f in files:
+        if os.path.exists(f):
+            os.remove(f)
 
 
 def test_plotEnrichment_default():
-    plotfile = NamedTemporaryFile(suffix='.png', prefix='deeptools_testfile_', delete=False)
-    txtfile = NamedTemporaryFile(suffix='.tab', prefix='deeptools_testfile_', delete=False)
+    """Test default plotEnrichment output and raw counts."""
+
+    plotfile, txtfile = run_plotEnrichment()
 
-    for fmat in ["bam", "cram"]:
-        args = "--bamfiles {0}test1.{3} {0}test2.{3} --BED {0}test.gtf --plotFile {1}" \
-               " --plotFileFormat png --outRawCounts {2}".format(TEST_DATA, plotfile.name, txtfile.name, fmat ).split()
-        deeptools.plotEnrichment.main(args)
+    try:
+        assert filecmp.cmp(
+            os.path.join(ROOT, "outRawCounts_default.tabular"),
+            txtfile
+        ) is True
 
-        if fmat == "bam":
-            assert filecmp.cmp(os.path.join(ROOT, 'outRawCounts_default.tabular'), txtfile.name) is True
+        res = compare_images(
+            os.path.join(ROOT, "plotEnrichment_defaults.png"),
+            plotfile,
+            tolerance
+        )
 
-        res = compare_images(ROOT + 'plotEnrichment_defaults.png', plotfile.name, tolerance)
         assert res is None, res
+
+    finally:
+        cleanup(plotfile, txtfile)
+
+
+def test_plotEnrichment_ggplot():
+    """Test plotEnrichment output with --ggplot."""
+
+    plotfile, txtfile = run_plotEnrichment(
+        ["--ggplot"]
+    )
+
+    try:
+        res = compare_images(
+            os.path.join(ROOT, "plotEnrichment_ggplot.png"),
+            plotfile,
+            tolerance
+        )
+
+        assert res is None, res
+
+    finally:
+        cleanup(plotfile, txtfile)
\ No newline at end of file
diff --git a/pydeeptools/deeptools/test/test_plotEnrichment/deeptools_testfile_mhh5o0g9.png b/pydeeptools/deeptools/test/test_plotEnrichment/deeptools_testfile_mhh5o0g9.png
new file mode 100644
index 0000000000..5f215ec9d0
Binary files /dev/null and b/pydeeptools/deeptools/test/test_plotEnrichment/deeptools_testfile_mhh5o0g9.png differ
diff --git a/pydeeptools/deeptools/test/test_plotEnrichment/plotEnrichment_defaults.png b/pydeeptools/deeptools/test/test_plotEnrichment/plotEnrichment_defaults.png
index 6f0f6f3caf..a804a7b25f 100644
Binary files a/pydeeptools/deeptools/test/test_plotEnrichment/plotEnrichment_defaults.png and b/pydeeptools/deeptools/test/test_plotEnrichment/plotEnrichment_defaults.png differ
diff --git a/pydeeptools/deeptools/test/test_plotEnrichment/plotEnrichment_ggplot.png b/pydeeptools/deeptools/test/test_plotEnrichment/plotEnrichment_ggplot.png
new file mode 100644
index 0000000000..393b4b375e
Binary files /dev/null and b/pydeeptools/deeptools/test/test_plotEnrichment/plotEnrichment_ggplot.png differ
diff --git a/pydeeptools/deeptools/test/test_plotFingerprint.py b/pydeeptools/deeptools/test/test_plotFingerprint.py
index 81e1df33fe..37fb0068d6 100644
--- a/pydeeptools/deeptools/test/test_plotFingerprint.py
+++ b/pydeeptools/deeptools/test/test_plotFingerprint.py
@@ -1,53 +1,140 @@
 import os
-import filecmp
-from matplotlib.testing.compare import compare_images
 from tempfile import NamedTemporaryFile
+
+from matplotlib.testing.compare import compare_images
+
 import deeptools.plotFingerprint
 
+
 TEST_DATA = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
 ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_plotFingerprint/"
 
-print (TEST_DATA)
-print(ROOT)
 tolerance = 13
 
-def test_plotFingerprint_default():
-    plotfile = NamedTemporaryFile(suffix='.png', prefix='deeptools_testfile_', delete=False)
-    args = "-b {0}test1.bam {0}test2.bam -o {1} --plotFileFormat png -l test1 test2".format(TEST_DATA, plotfile.name).split()
+
+def run_plotFingerprint(args):
+    """Run plotFingerprint and return generated plot file."""
+
+    plotfile = NamedTemporaryFile(
+        suffix=".png",
+        prefix="deeptools_testfile_",
+        delete=False
+    )
+
+    args.extend([
+        "-o",
+        plotfile.name,
+        "--plotFileFormat",
+        "png"
+    ])
+
     deeptools.plotFingerprint.main(args)
 
-    res = compare_images(ROOT + 'test_plotFingerprint_default.png', plotfile.name, tolerance)
+    return plotfile.name
+
+
+def cleanup(*files):
+    for file in files:
+        if os.path.exists(file):
+            os.remove(file)
+
+
+def test_plotFingerprint_default():
+    """Image comparison test for default plotFingerprint output."""
+
+    args = (
+        f"-b {TEST_DATA}test1.bam {TEST_DATA}test2.bam "
+        "-l test1 test2"
+    ).split()
 
-    assert res is None, res
+    plotfile = run_plotFingerprint(args)
 
-    os.remove(plotfile.name)
+    try:
+        res = compare_images(
+            ROOT + "test_plotFingerprint_default.png",
+            plotfile,
+            tolerance
+        )
+
+        assert res is None, res
+
+    finally:
+        cleanup(plotfile)
+
+
+def test_plotFingerprint_ggplot():
+    """Image comparison test for --ggplot output."""
+
+    args = (
+        f"-b {TEST_DATA}test1.bam {TEST_DATA}test2.bam "
+        "-l test1 test2 "
+        "--ggplot"
+    ).split()
+
+    plotfile = run_plotFingerprint(args)
+
+    try:
+        res = compare_images(
+            ROOT + "test_plotFingerprint_ggplot.png",
+            plotfile,
+            tolerance
+        )
+
+        assert res is None, res
+
+    finally:
+        cleanup(plotfile)
 
 
 def test_plotFingerprint_quality_metrics_and_JSD():
     """
-    Test --outQualityMetrics together with --JSDsample. Neither the quality
-    metrics table nor the JS-distance computation was covered elsewhere.
+    Test --outQualityMetrics together with --JSDsample.
     """
-    plotfile = NamedTemporaryFile(suffix='.png', prefix='deeptools_testfile_', delete=False)
-    qcfile = NamedTemporaryFile(suffix='.tab', prefix='deeptools_testfile_', delete=False)
-    args = ("-b {0}test1.bam {0}test2.bam -o {1} --plotFileFormat png -l test1 test2 "
-            "--outQualityMetrics {2} --JSDsample {0}test1.bam".format(TEST_DATA, plotfile.name, qcfile.name)).split()
-    deeptools.plotFingerprint.main(args)
 
-    with open(qcfile.name) as _foo:
-        lines = [line.rstrip("\n").split("\t") for line in _foo]
+    plotfile = NamedTemporaryFile(
+        suffix=".png",
+        prefix="deeptools_testfile_",
+        delete=False
+    )
+
+    qcfile = NamedTemporaryFile(
+        suffix=".tab",
+        prefix="deeptools_testfile_",
+        delete=False
+    )
+
+    args = (
+        f"-b {TEST_DATA}test1.bam {TEST_DATA}test2.bam "
+        f"-o {plotfile.name} "
+        "--plotFileFormat png "
+        "-l test1 test2 "
+        f"--outQualityMetrics {qcfile.name} "
+        f"--JSDsample {TEST_DATA}test1.bam"
+    ).split()
+
+    try:
+        deeptools.plotFingerprint.main(args)
+
+        with open(qcfile.name) as _foo:
+            lines = [
+                line.rstrip("\n").split("\t")
+                for line in _foo
+            ]
+
+        assert len(lines) == 3, f"expected 3 lines, got {len(lines)}"
+
+        header = lines[0]
+        auc = header.index("AUC")
+        jsd = header.index("JS Distance")
 
-    # header + one row per sample
-    assert len(lines) == 3, f"expected 3 lines, got {len(lines)}"
-    header = lines[0]
-    auc = header.index("AUC")
-    jsd = header.index("JS Distance")
+        rows = {
+            row[0]: row
+            for row in lines[1:]
+        }
 
-    rows = {row[0]: row for row in lines[1:]}
-    assert abs(float(rows["test1"][auc]) - 0.39310288701202156) < 1e-4
-    assert abs(float(rows["test2"][auc]) - 0.3641251150405128) < 1e-4
-    # JS distance of the JSDsample (test1) against itself is nan; test2 is finite
-    assert abs(float(rows["test2"][jsd]) - 0.078613413909822) < 1e-4
+        assert abs(float(rows["test1"][auc]) - 0.39310288701202156) < 1e-4
+        assert abs(float(rows["test2"][auc]) - 0.3641251150405128) < 1e-4
+        assert abs(float(rows["test2"][jsd]) - 0.078613413909822) < 1e-4
 
-    os.remove(plotfile.name)
-    os.remove(qcfile.name)
\ No newline at end of file
+    finally:
+        cleanup(plotfile.name, qcfile.name)
\ No newline at end of file
diff --git a/pydeeptools/deeptools/test/test_plotFingerprint/test_plotFingerprint_default.png b/pydeeptools/deeptools/test/test_plotFingerprint/test_plotFingerprint_default.png
index 1251a4f0bb..1959652782 100644
Binary files a/pydeeptools/deeptools/test/test_plotFingerprint/test_plotFingerprint_default.png and b/pydeeptools/deeptools/test/test_plotFingerprint/test_plotFingerprint_default.png differ
diff --git a/pydeeptools/deeptools/test/test_plotFingerprint/test_plotFingerprint_ggplot.png b/pydeeptools/deeptools/test/test_plotFingerprint/test_plotFingerprint_ggplot.png
new file mode 100644
index 0000000000..194f75d56a
Binary files /dev/null and b/pydeeptools/deeptools/test/test_plotFingerprint/test_plotFingerprint_ggplot.png differ
diff --git a/pydeeptools/deeptools/test/test_plotHeatmap.py b/pydeeptools/deeptools/test/test_plotHeatmap.py
index a111089945..008f567a5c 100644
--- a/pydeeptools/deeptools/test/test_plotHeatmap.py
+++ b/pydeeptools/deeptools/test/test_plotHeatmap.py
@@ -1,22 +1,114 @@
 import os
 import tempfile
+
+import matplotlib.pyplot as plt
 from matplotlib.testing.compare import compare_images
+
 import deeptools.plotHeatmap
 
-TEST_DATA = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_plotHeatmap/"
 
-print (TEST_DATA)
-print(ROOT)
-tolerance = 13
+TEST_DATA = os.path.join(os.path.dirname(os.path.abspath(__file__)), "test_data")
+ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), "test_plotHeatmap")
+
+# Headroom for anti-aliasing/text-hinting drift between matplotlib patch
+# versions (e.g. 3.10.x vs 3.11.x render identical plots with slightly
+# different sub-pixel edges); see matplotlib_defaults.py.
+tolerance = 25
 
-def test_plotHeatmap_default():
-    _, plotfile = tempfile.mkstemp(suffix=".png")
 
-    args = f"--matrixFile {TEST_DATA}computeMatrix_result1.gz --outFileName {plotfile}".split()
+def run_plotHeatmap(args):
+    """Run plotHeatmap and return generated output file."""
 
+    fd, plotfile = tempfile.mkstemp(suffix=".png")
+    # os.close(fd)
+
+    args = args + [
+        "--outFileName",
+        plotfile
+    ]
+
+    plt.ioff()
     deeptools.plotHeatmap.main(args)
+    
+    return plotfile
+
+
+# def run_plotHeatmap(args, Typ):
+    
+#     plotfile = os.path.join(
+#         ROOT,
+#         "debug"+ Typ + ".png"
+#     )
+
+#     if os.path.exists(plotfile):
+#         os.remove(plotfile)
+
+#     args = args + [
+#         "--outFileName",
+#         plotfile
+#     ]
+
+#     plt.ioff()
+#     deeptools.plotHeatmap.main(args)
+
+#     print("Generated:", plotfile)
+
+#     return plotfile
+
+
+def cleanup(plotfile):
+    plt.close("all")
+    if os.path.exists(plotfile):
+        os.remove(plotfile)
+
+
+def test_plotHeatmap_default():
+    """Image comparison test for default output."""
+
+    args = (
+        f"--matrixFile {TEST_DATA}/computeMatrix_result1.gz"
+    ).split()
+
+    plotfile = run_plotHeatmap(args)
+
+    try:
+        res = compare_images(
+            os.path.join(ROOT, "plotHeatmap_default.png"),
+            plotfile,
+            tolerance
+        )
+
+        assert res is None, (
+            f"{plotfile} doesn't match "
+            f"{ROOT}/plotHeatmap_default.png"
+        )
+
+    finally:
+        cleanup(plotfile)
+
+
+def test_plotHeatmap_ggplot():
+    """Check that --ggplot produces an output image."""
+
+    args = (
+        f"--matrixFile {TEST_DATA}/computeMatrix_result1.gz "
+        "--ggplot"
+    ).split()
+
+    plotfile = run_plotHeatmap(args)
+
+    try:
+        res = compare_images(
+            os.path.join(ROOT, "plotHeatmap_ggplot.png"),
+            plotfile,
+            tolerance
+        )
+
+        assert res is None, (
+            f"{plotfile} doesn't match "
+            f"{ROOT}/plotHeatmap_ggplot.png"
+        )
+
 
-    # assert filecmp.cmp(os.path.join(ROOT, 'outMatrix_default.tab'), txtfile.name) is True
-    res = compare_images(ROOT + 'plotHeatmap_default.png', plotfile, tolerance)
-    assert res is None, f"{plotfile} doesn't match {ROOT}plotHeatmap_default.png"
+    finally:
+        cleanup(plotfile)
\ No newline at end of file
diff --git a/pydeeptools/deeptools/test/test_plotHeatmap/plotHeatmap_default.png b/pydeeptools/deeptools/test/test_plotHeatmap/plotHeatmap_default.png
index 11e3989da6..35580dc99e 100644
Binary files a/pydeeptools/deeptools/test/test_plotHeatmap/plotHeatmap_default.png and b/pydeeptools/deeptools/test/test_plotHeatmap/plotHeatmap_default.png differ
diff --git a/pydeeptools/deeptools/test/test_plotHeatmap/plotHeatmap_ggplot.png b/pydeeptools/deeptools/test/test_plotHeatmap/plotHeatmap_ggplot.png
new file mode 100644
index 0000000000..79ea48ccdb
Binary files /dev/null and b/pydeeptools/deeptools/test/test_plotHeatmap/plotHeatmap_ggplot.png differ
diff --git a/pydeeptools/deeptools/test/test_plotPCA.py b/pydeeptools/deeptools/test/test_plotPCA.py
index c6bd269a5c..a284677764 100644
--- a/pydeeptools/deeptools/test/test_plotPCA.py
+++ b/pydeeptools/deeptools/test/test_plotPCA.py
@@ -256,3 +256,45 @@ def test_plotPCA_log2_and_rowCenter_affect_output():
     rowcenter = _run_pca(["--rowCenter"])
     assert not np.allclose(default[:, -1], log2[:, -1]), "--log2 was a no-op"
     assert not np.allclose(default[:, -1], rowcenter[:, -1]), "--rowCenter was a no-op"
+
+
+def test_plotPCA_ggplot():
+    """Image comparison test for --ggplot output."""
+
+    plotfile = NamedTemporaryFile(
+        suffix='.png',
+        prefix='deeptools_testfile_',
+        delete=False
+    )
+
+    tsvfile = NamedTemporaryFile(
+        suffix='.tsv',
+        prefix='deeptools_testfile_',
+        delete=False
+    )
+
+    args = (
+        "-in {0}test_samples.npz "
+        "-o {1} "
+        "--outFileNameData {2} "
+        "--ggplot"
+    ).format(
+        TEST_DATA,
+        plotfile.name,
+        tsvfile.name
+    ).split()
+
+    try:
+        deeptools.plotPCA.main(args)
+
+        res = compare_images(
+            ROOT + "test_plotPCA_ggplot.png",
+            plotfile.name,
+            tolerance
+        )
+
+        assert res is None, res
+
+    finally:
+        os.remove(plotfile.name)
+        os.remove(tsvfile.name)
\ No newline at end of file
diff --git a/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_default.png b/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_default.png
index 61833f0da7..e27190e1c4 100644
Binary files a/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_default.png and b/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_default.png differ
diff --git a/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_ggplot.png b/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_ggplot.png
new file mode 100644
index 0000000000..283f5e1845
Binary files /dev/null and b/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_ggplot.png differ
diff --git a/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_ggplot.tsv b/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_ggplot.tsv
new file mode 100644
index 0000000000..9822010ab4
--- /dev/null
+++ b/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_ggplot.tsv
@@ -0,0 +1,7 @@
+Component	wt1	wt2	wt3	kd1	kd2	kd3	Eigenvalue
+1	-1.9593953629718677	0.05992632052266172	0.015514438980501043	0.360872626954001	-0.06417725736657884	0.012713770441428606	5.807692278755935
+2	-3.3594106951252853	-0.1453930968029286	-0.134748642812576	-0.012411165664076072	-0.12363598259528208	-0.060663076611996596	0.07423028883557839
+3	-2.335822964750958	0.09987722598713754	-0.03413541974064124	-0.07165342296216681	0.05170385813600347	0.1373257036829112	0.0489717777349372
+4	-0.30789783922401226	0.004185214180292798	-0.013424388619808516	0.051462455776524196	-0.07942877370987256	0.0745864450320923	0.036809415525390125
+5	-1.2801086861541353	-0.07795301634249786	-0.04768720563614555	-0.02321427427821972	-0.032405677000559435	0.07420665888684398	0.026706723301448902
+6	-3.127415384537607	0.17202014078313335	0.08493798982333509	0.01429353530978131	0.018508562924871238	0.15753396743432724	0.017613563942900885
diff --git a/pydeeptools/deeptools/test/test_plotProfile.py b/pydeeptools/deeptools/test/test_plotProfile.py
index 03da7e1c1a..2a8a60221c 100644
--- a/pydeeptools/deeptools/test/test_plotProfile.py
+++ b/pydeeptools/deeptools/test/test_plotProfile.py
@@ -1,22 +1,86 @@
 import os
-import filecmp
-from matplotlib.testing.compare import compare_images
 from tempfile import NamedTemporaryFile
+
+from matplotlib.testing.compare import compare_images
+
 import deeptools.plotProfile
-import deeptools.heatmapper_utilities
+
 
 TEST_DATA = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
 ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_plotProfile/"
 
-print (TEST_DATA)
-print(ROOT)
-tolerance = 13
+# Headroom for anti-aliasing/text-hinting drift between matplotlib patch
+# versions (e.g. 3.10.x vs 3.11.x render identical plots with slightly
+# different sub-pixel edges); see matplotlib_defaults.py.
+tolerance = 40
+
+
+def run_plotProfile(args):
+    """Run plotProfile and return generated plot file."""
+
+    plotfile = NamedTemporaryFile(
+        suffix='.png',
+        prefix='deeptools_testfile_',
+        delete=False
+    )
+
+    args += [
+        "--outFileName",
+        plotfile.name,
+        "--plotFileFormat",
+        "png"
+    ]
 
-def test_plotProfile_default():
-    plotfile = NamedTemporaryFile(suffix='.png', prefix='deeptools_testfile_', delete=False)
-    args = "--matrixFile {0}computeMatrix_result1.gz   --outFileName {1} --plotFileFormat png".format(TEST_DATA, plotfile.name).split()
     deeptools.plotProfile.main(args)
-    res = compare_images(ROOT + 'plotProfile_default.png', plotfile.name, tolerance)
 
+    return plotfile.name
+
+
+def cleanup(plotfile):
+    if os.path.exists(plotfile):
+        os.remove(plotfile)
+
+
+def test_plotProfile_default():
+    """Image comparison test for default plotProfile output."""
+
+    args = (
+        f"--matrixFile {TEST_DATA}computeMatrix_result1.gz"
+    ).split()
+
+    plotfile = run_plotProfile(args)
+
+    try:
+        res = compare_images(
+            ROOT + "plotProfile_default.png",
+            plotfile,
+            tolerance
+        )
+
+        assert res is None, res
+
+    finally:
+        print(plotfile)
+
+
+def test_plotProfile_ggplot():
+    """Image comparison test for --ggplot output."""
+
+    args = (
+        f"--matrixFile {TEST_DATA}computeMatrix_result1.gz "
+        "--ggplot"
+    ).split()
+
+    plotfile = run_plotProfile(args)
+
+    try:
+        res = compare_images(
+            ROOT + "plotProfile_ggplot.png",
+            plotfile,
+            tolerance
+        )
+
+        assert res is None, res
 
-    assert res is None, res
+    finally:
+        print(plotfile)
\ No newline at end of file
diff --git a/pydeeptools/deeptools/test/test_plotProfile/plotProfile_default.png b/pydeeptools/deeptools/test/test_plotProfile/plotProfile_default.png
index 5119f417bb..c9ad1236bd 100644
Binary files a/pydeeptools/deeptools/test/test_plotProfile/plotProfile_default.png and b/pydeeptools/deeptools/test/test_plotProfile/plotProfile_default.png differ
diff --git a/pydeeptools/deeptools/test/test_plotProfile/plotProfile_ggplot.png b/pydeeptools/deeptools/test/test_plotProfile/plotProfile_ggplot.png
new file mode 100644
index 0000000000..c30fa0e459
Binary files /dev/null and b/pydeeptools/deeptools/test/test_plotProfile/plotProfile_ggplot.png differ
diff --git a/pydeeptools/deeptools/test/test_plotcorrelation.py b/pydeeptools/deeptools/test/test_plotcorrelation.py
index 0d3f78c978..6cfc7051d7 100644
--- a/pydeeptools/deeptools/test/test_plotcorrelation.py
+++ b/pydeeptools/deeptools/test/test_plotcorrelation.py
@@ -10,6 +10,9 @@
 COR_PLOT_1 = ROOT + "plotCorrelation_result1.png"
 COR_PLOT_2 = ROOT + "plotCorrelation_result2.png"
 
+COR_PLOT_GG_1 = ROOT + "plotCorrelation_result1_ggplot.png"
+COR_PLOT_GG_2 = ROOT + "plotCorrelation_result2_ggplot.png"
+
 
 def test_correlation_plot_with_minimal_options():
     """
@@ -40,3 +43,33 @@ def test_correlation_plot_scatter():
 
     res = compare_images(COR_PLOT_2, out_png2, 50)
     assert res is None, "Plots do not match"
+
+def test_correlation_plot_with_minimal_options_ggplot():
+    """
+    Test minimal command line args for correlation plot
+    with output as correlation matrix along with matrix
+    """
+    _, out_matrix_gg = tempfile.mkstemp(suffix=".tsv")
+    _, out_png_gg = tempfile.mkstemp(suffix=".png")
+    args = "--corData {} -p heatmap -c pearson -o {}  --outFileCorMatrix {} --ggplot".format(COR_DATA_IN1, out_png_gg, out_matrix_gg).split()
+    pc.main(args)
+
+    _foo = open(out_matrix_gg, "r")
+    resp = _foo.readlines()[2]
+    _foo.close()
+    expected = "'bowtie2 test1.bam'\t1.0000\t1.0000\n"
+    assert expected in resp, f"'{expected}' not found in '{resp}'"
+
+    res = compare_images(COR_PLOT_GG_1, out_png_gg, 50)
+    assert res is None, "Plots do not match"
+
+def test_correlation_plot_scatter_ggplot():
+    """
+    Test command line args for correlation plot with output as scatter plot
+    """
+    _, out_png2_gg = tempfile.mkstemp(suffix=".png")
+    args = "--corData {} -p scatterplot -c pearson  -o {} --ggplot".format(COR_DATA_IN1, out_png2_gg).split()
+    pc.main(args)
+
+    res = compare_images(COR_PLOT_GG_2, out_png2_gg, 50)
+    assert res is None, "Plots do not match"
diff --git a/pyproject.toml b/pyproject.toml
index b2093f97a6..65d620e49a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,7 +51,12 @@ actions = [
     "twine",
     "build",
     "planemo",
-    "matplotlib == 3.11", # pin matplotlib version to avoid plots changing in pytests (font size defaults etc.)
+    # matplotlib 3.10.0-3.10.4 hit a Path.__deepcopy__ RecursionError on
+    # Python 3.14 for any marker-using plot (fixed upstream in 3.10.5).
+    # Baseline images are pinned against 3.11.0 rendering; image-comparison
+    # tests carry tolerance headroom for anti-aliasing/text-hinting drift
+    # between 3.10.x and 3.11.x point releases (see matplotlib_defaults.py).
+    "matplotlib >= 3.10.5, < 3.12",
 ]
 [project.urls]
 homepage = "https://pypi.python.org/pypi/deepTools/"