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extra == 'tests' - - pooch>=1.8.0 ; extra == 'tests' - - conda-lock==3.0.1 ; extra == 'maintenance' - requires_python: '>=3.11' - pypi: https://files.pythonhosted.org/packages/72/65/a4559d4ff4a210d2a26d7ca0712e4e738cbfc963135f86e8ae807ca420eb/pysam-0.24.0-cp314-cp314-macosx_11_0_arm64.whl name: pysam version: 0.24.0 @@ -4814,11 +4372,6 @@ packages: version: 0.3.25 sha256: 852c41f00afc610322eb3c5aba74068d05b340d09db4573db2deca330ad48f30 requires_python: '>=3.9' -- pypi: https://files.pythonhosted.org/packages/7b/91/984aca2ec129e2757d1e4e3c81c3fcda9d0f85b74670a094cc443d9ee949/joblib-1.5.3-py3-none-any.whl - name: joblib - version: 1.5.3 - sha256: 5fc3c5039fc5ca8c0276333a188bbd59d6b7ab37fe6632daa76bc7f9ec18e713 - requires_python: '>=3.9' - pypi: https://files.pythonhosted.org/packages/7c/03/b8cdb625a21f710dfa11bbca1f48fb4057d2c0286975f8b415bf80942c99/matplotlib-3.11.0-cp314-cp314-macosx_11_0_arm64.whl name: matplotlib version: 3.11.0 @@ -5330,70 +4883,6 @@ packages: name: deeptoolsintervals version: 0.1.9 sha256: 7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6 -- pypi: https://files.pythonhosted.org/packages/ac/20/75f915ff375d6249e6550ac740fdbbd66159a068fd3af1400ff62036b07a/scikit_learn-1.9.0-cp312-cp312-macosx_10_13_x86_64.whl - name: scikit-learn - version: 1.9.0 - sha256: 2bd41b0d201bc81575531b96b713d3eb5e5f50fb0b82101ff0f92294fdc236ac - requires_dist: - - numpy>=1.24.1 - - scipy>=1.10.0 - - joblib>=1.4.0 - - narwhals>=2.0.1 - - threadpoolctl>=3.5.0 - - numpy>=1.24.1 ; extra == 'build' - - scipy>=1.10.0 ; extra == 'build' - - cython>=3.1.2 ; extra == 'build' - - meson-python>=0.17.1 ; extra == 'build' - - numpy>=1.24.1 ; extra == 'install' - - scipy>=1.10.0 ; extra == 'install' - - joblib>=1.4.0 ; extra == 'install' - - narwhals>=2.0.1 ; extra == 'install' - - threadpoolctl>=3.5.0 ; extra == 'install' - - matplotlib>=3.6.1 ; extra == 'benchmark' - - pandas>=1.5.0 ; extra == 'benchmark' - - memory-profiler>=0.57.0 ; extra == 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b/pydeeptools/deeptools/bamPEFragmentSize.py index 362b118555..3f6db136c1 100755 --- a/pydeeptools/deeptools/bamPEFragmentSize.py +++ b/pydeeptools/deeptools/bamPEFragmentSize.py @@ -3,17 +3,11 @@ import argparse import sys - import matplotlib import numpy as np - -matplotlib.use("Agg") -matplotlib.rcParams["pdf.fonttype"] = 42 -matplotlib.rcParams["svg.fonttype"] = "none" +from deeptools import matplotlib_defaults from importlib.metadata import version - import matplotlib.pyplot as plt - from deeptools.getFragmentAndReadSize import get_read_and_fragment_length # own tools diff --git a/pydeeptools/deeptools/correlation.py b/pydeeptools/deeptools/correlation.py index 4d8ad36bc4..77a9ad37a3 100644 --- a/pydeeptools/deeptools/correlation.py +++ b/pydeeptools/deeptools/correlation.py @@ -4,10 +4,7 @@ import numpy as np import scipy.cluster.hierarchy as sch import scipy.stats -import matplotlib as mpl -mpl.use('Agg') -mpl.rcParams['pdf.fonttype'] = 42 -mpl.rcParams['svg.fonttype'] = 'none' +from deeptools import matplotlib_defaults import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec import matplotlib.ticker @@ -246,7 +243,7 @@ def plot_correlation(self, plot_filename, plot_title='', vmax=None, font_size = 5 else: font_size = int(14 - 0.25 * num_rows) - mpl.rcParams.update({'font.size': font_size}) + matplotlib.rcParams.update({'font.size': font_size}) # set the minimum and maximum values if vmax is None: vmax = 1 @@ -348,7 +345,6 @@ def plot_scatter(self, plot_filename, plot_title='', image_format=None, log1p=Fa grids = gridspec.GridSpec(num_samples, num_samples) grids.update(wspace=0, hspace=0) fig = plt.figure(figsize=(2 * num_samples, 2 * num_samples)) - plt.rcParams['font.size'] = 8.0 plt.suptitle(plot_title) if log1p is True: self.matrix = np.log1p(self.matrix) diff --git a/pydeeptools/deeptools/correlation_heatmap.py b/pydeeptools/deeptools/correlation_heatmap.py index 58dbdfbc04..690717ee95 100644 --- a/pydeeptools/deeptools/correlation_heatmap.py +++ b/pydeeptools/deeptools/correlation_heatmap.py @@ -1,15 +1,11 @@ -from matplotlib import use as mplt_use -mplt_use('Agg') +from deeptools import matplotlib_defaults from deeptools import cm # noqa: F401 import matplotlib.pyplot as plt import numpy as np import scipy.cluster.hierarchy as sch -from matplotlib import rcParams import matplotlib.colors as pltcolors import copy -rcParams['pdf.fonttype'] = 42 -rcParams['svg.fonttype'] = 'none' old_settings = np.seterr(all='ignore') @@ -26,7 +22,7 @@ def plot_correlation(corr_matrix, labels, plotFileName, vmax=None, font_size = 5 else: font_size = int(14 - 0.25 * num_rows) - rcParams.update({'font.size': font_size}) + matplotlib.rcParams.update({'font.size': font_size}) # set the minimum and maximum values if vmax is None: vmax = 1 diff --git a/pydeeptools/deeptools/heatmapper_utilities.py b/pydeeptools/deeptools/heatmapper_utilities.py index 39256b5fdc..130de0945f 100644 --- a/pydeeptools/deeptools/heatmapper_utilities.py +++ b/pydeeptools/deeptools/heatmapper_utilities.py @@ -1,8 +1,5 @@ import numpy as np -import matplotlib -matplotlib.use('Agg') -matplotlib.rcParams['pdf.fonttype'] = 42 -matplotlib.rcParams['svg.fonttype'] = 'none' +from deeptools import matplotlib_defaults import matplotlib.colors as pltcolors import textwrap diff --git a/pydeeptools/deeptools/matplotlib_defaults.py b/pydeeptools/deeptools/matplotlib_defaults.py new file mode 100644 index 0000000000..4b62527352 --- /dev/null +++ b/pydeeptools/deeptools/matplotlib_defaults.py @@ -0,0 +1,22 @@ +import matplotlib + +# Backend should 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.size": 8.0, + + # Figure defaults + "figure.dpi": 100, + "savefig.dpi": 200, +}) + + diff --git a/pydeeptools/deeptools/plotCorrelation.py b/pydeeptools/deeptools/plotCorrelation.py index c9ec13e670..1aa7118e9a 100644 --- a/pydeeptools/deeptools/plotCorrelation.py +++ b/pydeeptools/deeptools/plotCorrelation.py @@ -4,10 +4,7 @@ import sys import argparse import numpy as np -import matplotlib -matplotlib.use('Agg') -matplotlib.rcParams['pdf.fonttype'] = 42 -matplotlib.rcParams['svg.fonttype'] = 'none' +from deeptools import matplotlib_defaults import matplotlib.pyplot as plt from importlib.metadata import version from deeptools.correlation import Correlation diff --git a/pydeeptools/deeptools/plotCoverage.py b/pydeeptools/deeptools/plotCoverage.py index 0b6df5b4a0..4cf2ca144b 100755 --- a/pydeeptools/deeptools/plotCoverage.py +++ b/pydeeptools/deeptools/plotCoverage.py @@ -5,11 +5,7 @@ import sys import argparse import numpy as np - -import matplotlib -matplotlib.use('Agg') -matplotlib.rcParams['pdf.fonttype'] = 42 -matplotlib.rcParams['svg.fonttype'] = 'none' +from deeptools import matplotlib_defaults import matplotlib.pyplot as plt from importlib.metadata import version import deeptools.countReadsPerBin as countR diff --git a/pydeeptools/deeptools/plotEnrichment.py b/pydeeptools/deeptools/plotEnrichment.py index d1d0c1e75d..26c9d590c8 100755 --- a/pydeeptools/deeptools/plotEnrichment.py +++ b/pydeeptools/deeptools/plotEnrichment.py @@ -4,10 +4,7 @@ import sys import argparse import numpy as np -import matplotlib -matplotlib.use('Agg') -matplotlib.rcParams['pdf.fonttype'] = 42 -matplotlib.rcParams['svg.fonttype'] = 'none' +from deeptools import matplotlib_defaults import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec diff --git a/pydeeptools/deeptools/plotFingerprint.py b/pydeeptools/deeptools/plotFingerprint.py index f0756bc2a8..5600e8c4db 100755 --- a/pydeeptools/deeptools/plotFingerprint.py +++ b/pydeeptools/deeptools/plotFingerprint.py @@ -4,10 +4,7 @@ import sys import argparse import numpy as np -import matplotlib -matplotlib.use('Agg') -matplotlib.rcParams['pdf.fonttype'] = 42 -matplotlib.rcParams['svg.fonttype'] = 'none' +from deeptools import matplotlib_defaults import matplotlib.pyplot as plt from scipy import interpolate from scipy.stats import poisson diff --git a/pydeeptools/deeptools/plotHeatmap.py b/pydeeptools/deeptools/plotHeatmap.py index 5cbbb51550..a23aa8e1ea 100755 --- a/pydeeptools/deeptools/plotHeatmap.py +++ b/pydeeptools/deeptools/plotHeatmap.py @@ -6,9 +6,7 @@ from collections import OrderedDict import numpy as np import matplotlib -matplotlib.use('Agg') -matplotlib.rcParams['pdf.fonttype'] = 42 -matplotlib.rcParams['svg.fonttype'] = 'none' +from deeptools import matplotlib_defaults import matplotlib.pyplot as plt from matplotlib.font_manager import FontProperties import matplotlib.gridspec as gridspec @@ -290,8 +288,9 @@ def plotMatrix(hm, outFileName, yMin = [yMin] if not isinstance(yMax, list): yMax = [yMax] + + plt.rcParams['font.size'] = matplotlib.rcParams['font.size'] - plt.rcParams['font.size'] = 8.0 fontP = FontProperties() showSummaryPlot = False diff --git a/pydeeptools/deeptools/plotPCA.py b/pydeeptools/deeptools/plotPCA.py index 1532706cac..24260b2c79 100644 --- a/pydeeptools/deeptools/plotPCA.py +++ b/pydeeptools/deeptools/plotPCA.py @@ -3,10 +3,7 @@ import sys import argparse -import matplotlib -matplotlib.use('Agg') -matplotlib.rcParams['pdf.fonttype'] = 42 -matplotlib.rcParams['svg.fonttype'] = 'none' +from deeptools import matplotlib_defaults from importlib.metadata import version from deeptools.correlation import Correlation from deeptools.parserCommon import writableFile, expand_list diff --git a/pydeeptools/deeptools/plotProfile.py b/pydeeptools/deeptools/plotProfile.py index 53ed0625b9..0371208c4e 100755 --- a/pydeeptools/deeptools/plotProfile.py +++ b/pydeeptools/deeptools/plotProfile.py @@ -7,10 +7,7 @@ import argparse import numpy as np from math import ceil -import matplotlib -matplotlib.use('Agg') -matplotlib.rcParams['pdf.fonttype'] = 42 -matplotlib.rcParams['svg.fonttype'] = 'none' +from deeptools import matplotlib_defaults import matplotlib.pyplot as plt from matplotlib.font_manager import FontProperties from matplotlib import colors as pltcolors @@ -178,7 +175,6 @@ def __init__(self, hm, out_file_name, cols = self.numplots self.grids = gridspec.GridSpec(rows, cols) - plt.rcParams['font.size'] = 8.0 self.font_p = FontProperties() self.font_p.set_size('small') diff --git a/pydeeptools/deeptools/test/test_data/bamPEFragmentSize_histogram_result1.png b/pydeeptools/deeptools/test/test_data/bamPEFragmentSize_histogram_result1.png index 8268288a32..fbc0dc7f4c 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 a212f44e5b..85d1fc134c 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_result2.png b/pydeeptools/deeptools/test/test_data/plotCorrelation_result2.png index db092d9bde..343ae41ba4 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_plotCoverage/plotCoverage_default.png b/pydeeptools/deeptools/test/test_plotCoverage/plotCoverage_default.png index f0f57324ef..8e8e8b1c58 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_plotEnrichment/plotEnrichment_defaults.png b/pydeeptools/deeptools/test/test_plotEnrichment/plotEnrichment_defaults.png index 6f0f6f3caf..e379baf838 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_plotFingerprint/test_plotFingerprint_default.png b/pydeeptools/deeptools/test/test_plotFingerprint/test_plotFingerprint_default.png index 78824da9fe..275b8087c3 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_plotHeatmap/plotHeatmap_default.png b/pydeeptools/deeptools/test/test_plotHeatmap/plotHeatmap_default.png index 606c1b4e22..726fdc1f3d 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_plotPCA/test_plotPCA_default.png b/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_default.png index ec90f17dfb..61833f0da7 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_default.tsv b/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_default.tsv index 818ee46c6d..2825477a63 100644 --- a/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_default.tsv +++ b/pydeeptools/deeptools/test/test_plotPCA/test_plotPCA_default.tsv @@ -1,7 +1,7 @@ Component wt1 wt2 wt3 kd1 kd2 kd3 Eigenvalue -1 -1.9593953629718786 -0.05992632052266235 0.01551443898050737 0.36087262695399747 -0.06417725736658209 0.012713770441420403 5.807692278755936 -2 -3.359410695125286 0.14539309680293142 -0.13474864281257853 -0.01241116566407577 -0.12363598259527717 -0.060663076611993313 0.07423028883557825 -3 -2.335822964750958 -0.09987722598713865 -0.034135419740642575 -0.07165342296216214 0.051703858136008 0.13732570368291072 0.04897177773493676 -4 -0.3078978392240127 -0.004185214180292649 -0.013424388619809194 0.05146245577652413 -0.0794287737098722 0.07458644503209262 0.03680941552538939 -5 -1.280108686154136 0.07795301634249859 -0.047687205636145584 -0.023214274278218 -0.03240567700055615 0.0742066588868442 0.026706723301448194 -6 -3.1274153845376063 -0.17202014078313513 0.08493798982333466 0.014293535309782638 0.018508562924869645 0.1575339674343244 0.017613563942900697 +1 -1.9593953629718786 -0.0599263205226625 0.015514438980507314 0.3608726269539977 -0.06417725736658203 0.012713770441420292 5.807692278755936 +2 -3.359410695125286 0.1453930968029311 -0.13474864281257853 -0.012411165664075682 -0.12363598259527717 -0.060663076611993313 0.07423028883557825 +3 -2.335822964750958 -0.0998772259871388 -0.03413541974064263 -0.07165342296216205 0.05170385813600817 0.13732570368291072 0.04897177773493676 +4 -0.3078978392240127 -0.004185214180292667 -0.013424388619809201 0.051462455776524134 -0.0794287737098722 0.07458644503209262 0.03680941552538939 +5 -1.280108686154136 0.0779530163424985 -0.04768720563614561 -0.023214274278217935 -0.0324056770005561 0.0742066588868442 0.026706723301448194 +6 -3.1274153845376063 -0.17202014078313563 0.08493798982333454 0.014293535309782737 0.01850856292486998 0.1575339674343244 0.017613563942900697 diff --git a/pydeeptools/deeptools/test/test_plotProfile/plotProfile_default.png b/pydeeptools/deeptools/test/test_plotProfile/plotProfile_default.png index f7ba808a38..7308a61d14 100644 Binary files a/pydeeptools/deeptools/test/test_plotProfile/plotProfile_default.png and b/pydeeptools/deeptools/test/test_plotProfile/plotProfile_default.png differ