centralized matplotlibs params and warnings from the plotter functions

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

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)

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

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
 

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,
+})
+
+

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

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

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
 

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

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

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

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')
 

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