huge update on look and backend of plots; easy make cmd for figure ge…

…neration added; scripts slightly modified; figures updated

conkit/plot/ContactMapPlot.py

@@ -13,7 +13,6 @@
 import numpy
 
 from conkit import constants
-from conkit.core import ContactMap
 from conkit.plot._Figure import Figure
 
 
@@ -25,59 +24,92 @@ def __init__(self, hierarchy, other=None, reference=None, altloc=False, use_conf
         Parameters
         ----------
         hierarchy : :obj:`conkit.core.ContactMap`
-           A ConKit :obj:`conkit.core.ContactMap`
+           The default contact map hierarchy
         other : :obj:`conkit.core.ContactMap`, optional
-           A ConKit :obj:`conkit.core.ContactMap`
+           The second contact map hierarchy
         reference : :obj:`conkit.core.ContactMap`, optional
-           A ConKit :obj:`conkit.core.ContactMap` [this map refers to the reference contacts]
+           The reference contact map hierarchy
         altloc : bool, optional
            Use the res_altloc positions [default: False]
         use_conf : bool, optional
            The marker size will correspond to the raw score [default: False]
         **kwargs
            General :obj:`conkit.plot._Figure.Figure` keyword arguments
 
-        Raises
-        ------
-        RuntimeError
-           The hierarchy is not a :obj:`conkit.core.SequenceFile` object
-
         """
         super(ContactMapFigure, self).__init__(**kwargs)
 
-        if not isinstance(hierarchy, ContactMap):
-            raise RuntimeError("Provided hierarchy is not a ContactMap")
-        elif other and not isinstance(other, ContactMap):
-            raise RuntimeError("Provided other hierarchy is not a ContactMap")
-        elif reference and not isinstance(reference, ContactMap):
-            raise RuntimeError("Provided reference hierarchy is not a ContactMap")
+        self._hierarchy = None
+        self._other = None
+        self._reference = None
+
+        self.altloc = altloc
+        self.use_conf = use_conf
+
+        self.hierarchy = hierarchy
+        self.other = other
+        self.reference = reference
+
+        self._draw()
+
+    @property
+    def hierarchy(self):
+        """The default contact map hierarchy"""
+        return self._hierarchy
 
+    @hierarchy.setter
+    def hierarchy(self, hierarchy):
+        """Define the default contact map hierarchy"""
+        if hierarchy:
+            Figure._check_hierarchy(hierarchy, "ContactMap")
         self._hierarchy = hierarchy
-        self._other = other
-        self._reference = reference
-        self._altloc = altloc
-        self._use_conf = use_conf
 
+    @property
+    def other(self):
+        """The second contact map hierarchy"""
+        return self._other
+
+    @other.setter
+    def other(self, hierarchy):
+        """Define the default contact map hierarchy"""
+        if hierarchy:
+            Figure._check_hierarchy(hierarchy, "ContactMap")
+        self._other = hierarchy
+
+    @property
+    def reference(self):
+        """The reference contact map hierarchy"""
+        return self._reference
+
+    @reference.setter
+    def reference(self, hierarchy):
+        """Define the reference contact map hierarchy"""
+        if hierarchy:
+            Figure._check_hierarchy(hierarchy, "ContactMap")
+        self._reference = hierarchy
+
+    def redraw(self):
+        """Re-draw the plot with updated parameters"""
         self._draw()
 
-    def draw(self):
+    def _draw(self):
         """Draw the actual plot"""
 
         fig, ax = matplotlib.pyplot.subplots(dpi=self.dpi)
 
         # Plot the other_ref contacts
         if self._reference:
-            if self._altloc:
+            if self.altloc:
                 reference_data = numpy.asarray([(c.res1_altseq, c.res2_altseq)
                                                 for c in self._reference if c.is_true_positive])
             else:
                 reference_data = numpy.asarray([(c.res1_seq, c.res2_seq)
                                                 for c in self._reference if c.is_true_positive])
             reference_colors = [constants.RFCOLOR for _ in range(len(reference_data))]
             ax.scatter(reference_data.T[0], reference_data.T[1], color=reference_colors,
-                       marker='.', edgecolor='none', linewidths=0.0)
+                       s=10, marker='o', edgecolor='none', linewidths=0.0)
             ax.scatter(reference_data.T[1], reference_data.T[0], color=reference_colors,
-                       marker='.', edgecolor='none', linewidths=0.0)
+                       s=10, marker='o', edgecolor='none', linewidths=0.0)
 
         # Plot the self contacts
         self_data = numpy.asarray([(c.res1_seq, c.res2_seq, c.raw_score) for c in self._hierarchy])
@@ -86,14 +118,14 @@ def draw(self):
             else constants.FPCOLOR if contact.is_false_positive
             else constants.NTCOLOR for contact in self._hierarchy
             ]
-        if self._use_conf:
-            # TODO: Find a better scaling algorithm
-            self_sizes = (self_data.T[2] - self_data.T[2].min()) / (self_data.T[2].max() - self_data.T[2].min()) * 500
+        if self.use_conf:
+            self_sizes = (self_data.T[2] - self_data.T[2].min()) / (self_data.T[2].max() - self_data.T[2].min())
+            self_sizes = self_sizes * 20 + 10
         else:
-            self_sizes = None
+            self_sizes = [10] * len(self_data.T[2])
 
         # This is the bottom triangle
-        ax.scatter(self_data.T[1], self_data.T[0], color=self_colors, marker='.',
+        ax.scatter(self_data.T[1], self_data.T[0], color=self_colors, marker='o',
                    s=self_sizes, edgecolor='none', linewidths=0.0)
 
         # Plot the other contacts
@@ -104,17 +136,17 @@ def draw(self):
                 else constants.FPCOLOR if contact.is_false_positive
                 else constants.NTCOLOR for contact in self._other
                 ]
-            if self._use_conf:
-                # TODO: Find a better scaling algorithm
-                other_sizes = (other_data.T[2] - other_data.T[2].min()) / (other_data.T[2].max() - other_data.T[2].min()) * 500
+            if self.use_conf:
+                other_sizes = (other_data.T[2] - other_data.T[2].min()) / (other_data.T[2].max() - other_data.T[2].min())
+                other_sizes = other_sizes * 20 + 10
             else:
-                other_sizes = None
+                other_sizes = [10] * len(other_data.T[2])
             # This is the upper triangle
-            ax.scatter(other_data.T[0], other_data.T[1], color=other_colors, marker='.',
+            ax.scatter(other_data.T[0], other_data.T[1], color=other_colors, marker='o',
                        s=other_sizes, edgecolor='none', linewidths=0.0)
         else:
             # This is the upper triangle
-            ax.scatter(self_data.T[0], self_data.T[1], color=self_colors, marker='.',
+            ax.scatter(self_data.T[0], self_data.T[1], color=self_colors, marker='o',
                        s=self_sizes, edgecolor='none', linewidths=0.0)
 
         # Allow dynamic x and y limits
@@ -140,11 +172,11 @@ def draw(self):
         # Create a custom legend
         if self._reference:
             tp_artist = matplotlib.pyplot.Line2D((0, 1), (0, 0), color=constants.TPCOLOR,
-                                                 marker='o', linestyle='', label='True positive')
+                                                 marker='o', linestyle='', label='Match')
             fp_artist = matplotlib.pyplot.Line2D((0, 1), (0, 0), color=constants.FPCOLOR,
-                                                 marker='o', linestyle='', label='False positive')
+                                                 marker='o', linestyle='', label='Mismatch')
             rf_artist = matplotlib.pyplot.Line2D((0, 1), (0, 0), color=constants.RFCOLOR,
-                                                 marker='o', linestyle='', label='Reference')
+                                                 marker='o', linestyle='', label='Structural')
             artists = [tp_artist, fp_artist, rf_artist]
         else:
             nt_artist = matplotlib.pyplot.Line2D((0, 1), (0, 0), color=constants.NTCOLOR,

conkit/plot/SequenceCoveragePlot.py

@@ -11,7 +11,6 @@
 import matplotlib.pyplot
 import numpy
 
-from conkit.core import SequenceFile
 from conkit.plot._Figure import Figure
 
 
@@ -27,24 +26,35 @@ def __init__(self, hierarchy, **kwargs):
         **kwargs
            General :obj:`conkit.plot._Figure.Figure` keyword arguments
 
-        Raises
-        ------
-        RuntimeError
-           The hierarchy is not an alignment
-        RuntimeError
-           The hierarchy is not a :obj:`conkit.core.SequenceFile` object
 
         """
         super(SequenceCoverageFigure, self).__init__(**kwargs)
+        self._hierarchy = hierarchy
+        self._draw()
 
-        if not isinstance(hierarchy, SequenceFile):
-            raise RuntimeError("Provided hierarchy is not a SequenceFile")
+    @property
+    def hierarchy(self):
+        """A ConKit :obj:`conkit.core.SequenceFile`"""
+        return self._hierarchy
 
-        if not hierarchy.is_alignment:
-            raise RuntimeError("Provided hierarchy does not show characteristics of an alignment")
+    @hierarchy.setter
+    def hierarchy(self, hierarchy):
+        """Define the ConKit :obj:`conkit.core.SequenceFile`
 
+        Raises
+        ------
+        RuntimeError
+           The hierarchy is not an alignment
+
+        """
+        if hierarchy:
+            Figure._check_hierarchy(hierarchy, "SequenceFile")
+            if not hierarchy.is_alignment:
+                raise RuntimeError("Provided hierarchy does not show characteristics of an alignment")
         self._hierarchy = hierarchy
 
+    def redraw(self):
+        """Re-draw the plot with updated parameters"""
         self._draw()
 
     def _draw(self):
@@ -54,15 +64,16 @@ def _draw(self):
         aa_frequencies = numpy.asarray(self._hierarchy.calculate_freq()) * self._hierarchy.top_sequence.seq_len
 
         fig, ax = matplotlib.pyplot.subplots(dpi=self.dpi)
-        ax.plot(residues, aa_frequencies, color='#000000', marker='.', linestyle='-',
-                label='Amino acid count')
+        ax.plot(residues, aa_frequencies, color='#000000', marker='o', linestyle='-',
+                markersize=5, label='Amino acid count')
 
         ax.axhline(self._hierarchy.top_sequence.seq_len * 0.3, color='r', label='30% Coverage')
         ax.axhline(self._hierarchy.top_sequence.seq_len * 0.6, color='g', label='60% Coverage')
 
         # Prettify the plot
-        ax.set_xticks(residues)
-        ax.set_xticklabels(residues)
+        xticks = numpy.arange(1, self._hierarchy.top_sequence.seq_len + 1, 5)
+        ax.set_xticks(xticks)
+        ax.set_xticklabels(xticks)
 
         ax.set_xlabel('Residue number')
         ax.set_ylabel('Sequence Count')

conkit/plot/_Figure.py

@@ -3,6 +3,12 @@
 __date__ = "07 Feb 2017"
 __version__ = 0.1
 
+from conkit.core import Contact
+from conkit.core import ContactMap
+from conkit.core import ContactFile
+from conkit.core import Sequence
+from conkit.core import SequenceFile
+
 
 class Figure(object):
     """A Figure class to store common features
@@ -100,3 +106,22 @@ def prefix(self):
     def prefix(self, prefix):
         """Define the prefix of the figure file"""
         self._prefix = prefix
+
+    @staticmethod
+    def _check_hierarchy(h, t):
+        """Check the hierarchy is of a specific type
+
+        Raises
+        ------
+        TypeError
+           Provided hierarchy is not of specified type
+        ValueError
+           Type is unknown
+
+        """
+        dict = {'Contact': Contact, 'ContactMap': ContactMap, 'ContactFile': ContactFile,
+                'Sequence': Sequence, 'SequenceFile': SequenceFile}
+        if t not in dict.keys():
+            raise ValueError("Type {0} is unknown".format(t))
+        elif not isinstance(h, dict[t]):
+            raise TypeError("Provided hierarchy is not a {0}".format(t))

conkit/plot/tests/test__Figure.py

@@ -0,0 +1,66 @@
+"""Testing facility for conkit.plot._Figure"""
+
+__author__ = "Felix Simkovic"
+__date__ = "08 Feb 2017"
+
+from conkit.plot._Figure import Figure
+
+import unittest
+
+
+class Test(unittest.TestCase):
+
+    def test__init__(self):
+        f = Figure()
+        self.assertEqual(300, f.dpi)
+        self.assertEqual("png", f.format)
+        self.assertEqual("conkit", f.prefix)
+
+        f = Figure(dpi=20, format="svg")
+        self.assertEqual(20, f.dpi)
+        self.assertEqual("svg", f.format)
+        self.assertEqual("conkit", f.prefix)
+
+        self.assertRaises(ValueError, Figure, format="ooo")
+
+    def test_dpi(self):
+        f = Figure()
+        self.assertEqual(300, f.dpi)
+        f.dpi = 20
+        self.assertEqual(20, f.dpi)
+
+    def test_filename(self):
+        f = Figure()
+        self.assertEqual("conkit.png", f.file_name)
+        f.file_name = "test.eps"
+        self.assertEqual("test.eps", f.file_name)
+        self.assertEqual("eps", f.format)
+        self.assertEqual("test", f.prefix)
+        f.format = "pdf"
+        self.assertEqual("test.pdf", f.file_name)
+        self.assertEqual("pdf", f.format)
+        self.assertEqual("test", f.prefix)
+        self.assertRaises(ValueError, setattr, f, "file_name", "test.ooo")
+
+    def test_format(self):
+        f = Figure()
+        self.assertEqual("png", f.format)
+        f.format = "pdf"
+        self.assertEqual("pdf", f.format)
+        f.format = "ps"
+        self.assertEqual("ps", f.format)
+        f.format = "png"
+        self.assertEqual("png", f.format)
+        self.assertRaises(ValueError, setattr, f, "format", "bbb")
+
+    def test_prefix(self):
+        f = Figure()
+        self.assertEqual("conkit", f.prefix)
+        f.prefix = "test"
+        self.assertEqual("test", f.prefix)
+        f.prefix = "/path/to/prefix"
+        self.assertEqual("/path/to/prefix", f.prefix)
+
+
+if __name__ == "__main__":
+    unittest.main(verbosity=2)

docs/Makefile

@@ -46,6 +46,7 @@ help:
 	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
 	@echo "  linkcheck  to check all external links for integrity"
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  figures    to create all figures used in the documentation"
 
 clean:
 	rm -rf $(BUILDDIR)/*
@@ -176,3 +177,12 @@ pseudoxml:
 	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
 	@echo
 	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+
+figures:
+	mkdir _tmp
+	git clone https://github.com/rigdenlab/conkit-examples.git _tmp/conkit-examples 
+	conkit.plot_map -o examples/images/toxd_cmap_simple.png _tmp/conkit-examples/toxd/toxd.fasta fasta _tmp/conkit-examples/toxd/toxd.mat ccmpred
+	conkit.plot_map -o examples/images/toxd_cmap_reference.png -p _tmp/conkit-examples/toxd/toxd.pdb _tmp/conkit-examples/toxd/toxd.fasta fasta _tmp/conkit-examples/toxd/toxd.mat ccmpred
+	conkit.plot_map -o examples/images/toxd_cmap_advanced.png -e _tmp/conkit-examples/toxd/toxd.psicov -ef psicov -p _tmp/conkit-examples/toxd/toxd.pdb _tmp/conkit-examples/toxd/toxd.fasta fasta _tmp/conkit-examples/toxd/toxd.mat ccmpred
+	conkit.plot_map -o examples/images/toxd_cmap_confidence.png --confidence -e _tmp/conkit-examples/toxd/toxd.psicov -ef psicov -p _tmp/conkit-examples/toxd/toxd.pdb _tmp/conkit-examples/toxd/toxd.fasta fasta _tmp/conkit-examples/toxd/toxd.mat ccmpred
+	rm -rf _tmp