Merge branch 'mh1/hex_colours' into 'master'

Allow specifying link colours as #rrggbb

See merge request !59

sails/circular_plots.py

@@ -12,6 +12,7 @@ import tempfile
 
 import numpy as np
 
+import matplotlib.colors as mc
 import matplotlib.pyplot as plt
 
 # Note that we currently assume the use of 1000 for band widths to make life
@@ -39,6 +40,8 @@ band_stroke_color     = white
 band_transparency     = 4
 </ideogram>
 
+{colors:s}
+
 {ticks:s}
 
 <image>
@@ -662,7 +665,7 @@ class CircosHandler(object):
                 if np.isnan(val):
                     continue
 
-                if isinstance(linkcolors, tuple):
+                if isinstance(linkcolors, (tuple, list)):
                     if val == 0:
                         color = linkcolors[0]
                     elif val < 0:
@@ -686,6 +689,89 @@ class CircosHandler(object):
 
         return '\n'.join(s)
 
+    def parse_colors(self, linkcolors, defaultlinkcolor):
+        """
+        Parse hex colours into something usable by circos
+        """
+
+        # Map (r, g, b) tuples to colour names
+        colour_dict = {}
+        colidx = 0
+
+        if isinstance(linkcolors, (tuple, list)):
+            lc = []
+            for colour in linkcolors:
+                if colour.startswith('#'):
+                    # Parse as #RGB and add to colour_dict
+                    r, g, b = mc.hex2color(colour)
+                    r = int(r * 255)
+                    g = int(g * 255)
+                    b = int(b * 255)
+
+                    if (r, g, b) not in colour_dict.keys():
+                        colour_dict[(r, g, b)] = 'customcolor{}'.format(colidx)
+                        colidx += 1
+
+                    lc.append(colour_dict[(r, g, b)])
+                else:
+                    # Leave as it is
+                    lc.append(colour)
+
+            lc = tuple(lc)
+        elif isinstance(linkcolors, np.ndarray):
+            lc = linkcolors.copy()
+
+            for row in range(lc.shape[0]):
+                for col in range(lc.shape[1]):
+                    colour = lc[row, col]
+                    if colour is not None and colour.startswith('#'):
+                        # Parse as #RGB and add to colour_dict
+                        r, g, b = mc.hex2color(colour)
+                        r = int(r * 255)
+                        g = int(g * 255)
+                        b = int(b * 255)
+
+                        if (r, g, b) not in colour_dict.keys():
+                            colour_dict[(r, g, b)] = 'customcolor{}'.format(colidx)
+                            colidx += 1
+
+                        lc[row, col] = colour_dict[(r, g, b)]
+
+        elif linkcolors is None:
+            lc = None
+        else:
+            raise Exception("Cannot parse link colors {}".format(linkcolors))
+
+        if defaultlinkcolor is None:
+            dlc = None
+        elif defaultlinkcolor.startswith("#"):
+            # Parse as #RGB and add to colour_dict
+            r, g, b = mc.hex2color(defaultlinkcolor)
+            r = int(r * 255)
+            g = int(g * 255)
+            b = int(b * 255)
+
+            if (r, g, b) not in colour_dict.keys():
+                colour_dict[(r, g, b)] = 'customcolor{}'.format(colidx)
+                colidx += 1
+
+            dlc = colour_dict[(r, g, b)]
+        else:
+            dlc = defaultlinkcolor
+
+        # Work out what to put in the colors section (if anything)
+        colour_text = ""
+
+        if len(colour_dict) > 0:
+            colour_text = """<colors>\n"""
+
+            for k, v in colour_dict.items():
+                colour_text += "{} = {},{},{}\n".format(v, k[0], k[1], k[2])
+
+            colour_text += """</colors>\n"""
+
+        return lc, dlc, colour_text
+
     def gen_circos_files(self, data, karyotype_name, output_name,
                          radius=1500,
                          circos_path='/etc/circos',
@@ -741,11 +827,13 @@ class CircosHandler(object):
         linkcolors = kwargs.get('linkcolors', None)
         defaultlinkcolor = kwargs.get('defaultlinkcolor', 'black')
 
+        lc, dlc, colors = self.parse_colors(linkcolors, defaultlinkcolor)
+
         circle_radius = kwargs.get('circle_prop', 0.85)
 
         # First of all, create the .txt links file
         f = open(linkspath, 'w')
-        f.write(self.links(data, linkcolors, defaultlinkcolor))
+        f.write(self.links(data, lc, dlc))
         f.close()
 
         # Now the config file - pass all keyword arguments down
@@ -755,6 +843,7 @@ class CircosHandler(object):
         f.write(CIRCOS_CONF_TEMPLATE.format(karyotype=karyotype_name,
                                             ticks=ticks,
                                             radius=radius,
+                                            colors=colors,
                                             circospath=circos_path,
                                             linksname=linksname,
                                             outputimage=imagename,