From ceef4301d8c7ac889825fb2d39c602611ab7328d Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Thu, 10 Dec 2015 17:45:13 +0000
Subject: [PATCH 01/16] Renamed matplotlib orientation parameter to invert_axes

---
 holoviews/plotting/bokeh/element.py |  4 +++-
 holoviews/plotting/mpl/chart.py     | 22 ++++++----------------
 holoviews/plotting/mpl/element.py   | 17 ++++++++++-------
 holoviews/plotting/mpl/plot.py      |  6 +++---
 holoviews/plotting/mpl/raster.py    |  2 +-
 5 files changed, 23 insertions(+), 28 deletions(-)

diff --git a/holoviews/plotting/bokeh/element.py b/holoviews/plotting/bokeh/element.py
index 8e3272ba72..f5d9166657 100644
--- a/holoviews/plotting/bokeh/element.py
+++ b/holoviews/plotting/bokeh/element.py
@@ -58,6 +58,9 @@ class ElementPlot(BokehPlot, GenericElementPlot):
 
           {'ticks': '20pt', 'title': '15pt', 'ylabel': '5px', 'xlabel': '5px'}""")
 
+    invert_axes = param.Boolean(default=False, doc="""
+        Whether to invert the x- and y-axis""")
+
     invert_xaxis = param.Boolean(default=False, doc="""
         Whether to invert the plot x-axis.""")
 
@@ -139,7 +142,6 @@ class ElementPlot(BokehPlot, GenericElementPlot):
 
     def __init__(self, element, plot=None, invert_axes=False,
                  show_labels=['x', 'y'], **params):
-        self.invert_axes = invert_axes
         self.show_labels = show_labels
         self.current_ranges = None
         super(ElementPlot, self).__init__(element, **params)
diff --git a/holoviews/plotting/mpl/chart.py b/holoviews/plotting/mpl/chart.py
index 2cd6547826..c9612727a5 100644
--- a/holoviews/plotting/mpl/chart.py
+++ b/holoviews/plotting/mpl/chart.py
@@ -291,7 +291,7 @@ def __init__(self, histograms, **params):
 
         super(HistogramPlot, self).__init__(histograms, **params)
 
-        if self.orientation == 'vertical':
+        if self.invert_axes:
             self.axis_settings = ['ylabel', 'xlabel', 'yticks']
         else:
             self.axis_settings = ['xlabel', 'ylabel', 'xticks']
@@ -309,7 +309,7 @@ def initialize_plot(self, ranges=None):
         # Get plot ranges and values
         edges, hvals, widths, lims = self._process_hist(hist)
 
-        if self.orientation == 'vertical':
+        if self.invert_axes:
             self.offset_linefn = self.handles['axis'].axvline
             self.plotfn = self.handles['axis'].barh
         else:
@@ -363,7 +363,7 @@ def _compute_ticks(self, element, edges, widths, lims):
     def get_extents(self, element, ranges):
         x0, y0, x1, y1 = super(HistogramPlot, self).get_extents(element, ranges)
         y0 = np.nanmin([0, y0])
-        return (y0, x0, y1, x1) if self.orientation == 'vertical' else (x0, y0, x1, y1)
+        return (x0, y0, x1, y1)
 
 
     def _process_axsettings(self, hist, lims, ticks):
@@ -390,7 +390,7 @@ def _update_artists(self, key, hist, edges, hvals, widths, lims, ranges):
         """
         plot_vals = zip(self.handles['artist'], edges, hvals, widths)
         for bar, edge, height, width in plot_vals:
-            if self.orientation == 'vertical':
+            if self.invert_axes:
                 bar.set_y(edge)
                 bar.set_width(height)
                 bar.set_height(width)
@@ -446,16 +446,6 @@ def _process_hist(self, hist):
         return edges, hvals, widths, lims
 
 
-    def _process_axsettings(self, hist, lims, ticks):
-        axsettings = super(SideHistogramPlot, self)._process_axsettings(hist, lims, ticks)
-        label = 'ylabel' if self.orientation == 'vertical' else 'xlabel'
-        if not self.show_xlabel:
-            axsettings[label] = ''
-        else:
-            axsettings[label] = str(hist.kdims[0])
-        return axsettings
-
-
     def _update_artists(self, n, element, edges, hvals, widths, lims, ranges):
         super(SideHistogramPlot, self)._update_artists(n, element, edges, hvals, widths, lims, ranges)
         self._update_plot(n, element, self.handles['artist'], lims, ranges)
@@ -494,7 +484,7 @@ def _update_plot(self, key, element, bars, lims, ranges):
     def get_extents(self, element, ranges):
         x0, _, x1, _ = element.extents
         _, y1 = element.range(1)
-        return (0, x0, y1, x1) if self.orientation == 'vertical' else (x0, 0, x1, y1)
+        return (x0, 0, x1, y1)
 
 
     def _colorize_bars(self, cmap, bars, element, main_range, dim):
@@ -521,7 +511,7 @@ def _update_separator(self, offset):
             offset_line.set_visible(False)
         else:
             offset_line.set_visible(True)
-            if self.orientation == 'vertical':
+            if self.invert_axes:
                 offset_line.set_xdata(offset)
             else:
                 offset_line.set_ydata(offset)
diff --git a/holoviews/plotting/mpl/element.py b/holoviews/plotting/mpl/element.py
index c5e87a26a9..9dfc455418 100644
--- a/holoviews/plotting/mpl/element.py
+++ b/holoviews/plotting/mpl/element.py
@@ -31,6 +31,11 @@ class ElementPlot(GenericElementPlot, MPLPlot):
     bgcolor = param.ClassSelector(class_=(str, tuple), default=None, doc="""
         If set bgcolor overrides the background color of the axis.""")
 
+    invert_axes = param.ObjectSelector(default=False, doc="""
+        Inverts the axes of the plot. Note that this parameter may not
+        always be respected by all plots but should be respected by
+        adjoined plots when appropriate.""")
+
     invert_xaxis = param.Boolean(default=False, doc="""
         Whether to invert the plot x-axis.""")
 
@@ -46,13 +51,6 @@ class ElementPlot(GenericElementPlot, MPLPlot):
     logz  = param.Boolean(default=False, doc="""
          Whether to apply log scaling to the y-axis of the Chart.""")
 
-    orientation = param.ObjectSelector(default='horizontal',
-                                       objects=['horizontal', 'vertical'], doc="""
-        The orientation of the plot. Note that this parameter may not
-        always be respected by all plots but should be respected by
-        adjoined plots when appropriate valid options are 'horizontal'
-        and 'vertical'.""")
-
     show_legend = param.Boolean(default=False, doc="""
         Whether to show legend for the plot.""")
 
@@ -139,6 +137,9 @@ def _finalize_axis(self, key, title=None, ranges=None, xticks=None, yticks=None,
                            if isinstance(sp.hmap, HoloMap))
             if element is not None and not suppress:
                 xlabel, ylabel, zlabel = self._axis_labels(element, subplots, xlabel, ylabel, zlabel)
+                if self.invert_axes:
+                    xlabel, ylabel = ylabel, xlabel
+
                 self._finalize_limits(axis, element, subplots, ranges)
 
                 # Tick formatting
@@ -227,6 +228,8 @@ def _finalize_limits(self, axis, view, subplots, ranges):
                     axis.set_zlim((zmin, zmax))
             else:
                 l, b, r, t = [coord if np.isreal(coord) else np.NaN for coord in extents]
+            if self.invert_axes:
+                l, b, r, t = b, l, t, r
             l, r = (c if np.isfinite(c) else None for c in (l, r))
             if self.invert_xaxis or any(p.invert_xaxis for p in subplots):
                 r, l = l, r
diff --git a/holoviews/plotting/mpl/plot.py b/holoviews/plotting/mpl/plot.py
index 974c88b2c9..9e4ea423d2 100644
--- a/holoviews/plotting/mpl/plot.py
+++ b/holoviews/plotting/mpl/plot.py
@@ -988,11 +988,11 @@ def _create_subplots(self, layout, positions, layout_dimensions, ranges, axes={}
                 if not isinstance(view, GridSpace):
                     override_opts = dict(aspect='square')
             elif pos == 'right':
-                right_opts = dict(orientation='vertical',
-                                  xaxis=None, yaxis='left')
+                right_opts = dict(invert_axes=True,
+                                  xaxis=None)
                 override_opts = dict(subplot_opts, **right_opts)
             elif pos == 'top':
-                top_opts = dict(xaxis='bottom', yaxis=None)
+                top_opts = dict(yaxis=None)
                 override_opts = dict(subplot_opts, **top_opts)
 
             # Override the plotopts as required
diff --git a/holoviews/plotting/mpl/raster.py b/holoviews/plotting/mpl/raster.py
index 4ba9c6da5d..abfeddf683 100644
--- a/holoviews/plotting/mpl/raster.py
+++ b/holoviews/plotting/mpl/raster.py
@@ -240,6 +240,7 @@ class RasterGridPlot(GridPlot, OverlayPlot):
     apply_ranges = param.Parameter(precedence=-1)
     apply_ticks = param.Parameter(precedence=-1)
     bgcolor = param.Parameter(precedence=-1)
+    invert_axes = param.Parameter(precedence=-1)
     invert_xaxis = param.Parameter(precedence=-1)
     invert_yaxis = param.Parameter(precedence=-1)
     legend_cols = param.Parameter(precedence=-1)
@@ -247,7 +248,6 @@ class RasterGridPlot(GridPlot, OverlayPlot):
     logx = param.Parameter(precedence=-1)
     logy = param.Parameter(precedence=-1)
     logz = param.Parameter(precedence=-1)
-    orientation = param.Parameter(precedence=-1)
     show_grid = param.Parameter(precedence=-1)
     style_grouping = param.Parameter(precedence=-1)
     xticks = param.Parameter(precedence=-1)

From 381ba64c97065b4523d7abc2f857314d02f86665 Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Thu, 10 Dec 2015 17:45:32 +0000
Subject: [PATCH 02/16] Avoid hardcoding PathPlot aspect option

---
 holoviews/plotting/mpl/path.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/holoviews/plotting/mpl/path.py b/holoviews/plotting/mpl/path.py
index a59c686ad5..cf0cd25ae4 100644
--- a/holoviews/plotting/mpl/path.py
+++ b/holoviews/plotting/mpl/path.py
@@ -9,10 +9,13 @@
 
 class PathPlot(ElementPlot):
 
+    aspect = param.Parameter(default='equal', doc="""
+        PathPlots axes usually define single space so aspect of Paths
+        follows aspect in data coordinates by default.""")
+
     style_opts = ['alpha', 'color', 'linestyle', 'linewidth', 'visible']
 
     def __init__(self, *args, **params):
-        self.aspect = 'equal'
         super(PathPlot, self).__init__(*args, **params)
 
     def initialize_plot(self, ranges=None):

From ac6bf2957a96c8a5496515338aa0d6a387891360 Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Thu, 10 Dec 2015 17:46:42 +0000
Subject: [PATCH 03/16] Added Spikes Element and plotting classes

---
 holoviews/element/chart.py           |  20 ++++++
 holoviews/plotting/bokeh/__init__.py |   7 +-
 holoviews/plotting/bokeh/chart.py    |  50 +++++++++++++
 holoviews/plotting/mpl/__init__.py   |   4 +-
 holoviews/plotting/mpl/chart.py      | 104 +++++++++++++++++++++++++++
 5 files changed, 181 insertions(+), 4 deletions(-)

diff --git a/holoviews/element/chart.py b/holoviews/element/chart.py
index f74902949b..5e5a01ab73 100644
--- a/holoviews/element/chart.py
+++ b/holoviews/element/chart.py
@@ -344,3 +344,23 @@ def __init__(self, data, **params):
         if isinstance(data, list) and all(isinstance(d, np.ndarray) for d in data):
             data = np.column_stack([d.flat if d.ndim > 1 else d for d in data])
         super(VectorField, self).__init__(data, **params)
+
+
+
+class Spikes(Chart):
+    """
+    Spikes is a 1D or 2D Element, which represents vertical or
+    horizontal ticks along some dimension.  If an additional dimension
+    is supplied it will be used to specify the height of the
+    lines. The Element may therefore be used to represent 1D
+    distributions, spectrograms or spike trains in electrophysiology.
+    """
+
+    group = param.String(default='Spikes', constant=True)
+
+    kdims = param.List(default=[Dimension('x')])
+
+    vdims = param.List(default=[])
+
+    _1d = True
+
diff --git a/holoviews/plotting/bokeh/__init__.py b/holoviews/plotting/bokeh/__init__.py
index e0aa6eb758..c1978d4e16 100644
--- a/holoviews/plotting/bokeh/__init__.py
+++ b/holoviews/plotting/bokeh/__init__.py
@@ -3,7 +3,7 @@
 from ...element import (Curve, Points, Scatter, Image, Raster, Path,
                         RGB, Histogram, Spread, HeatMap, Contours,
                         Path, Box, Bounds, Ellipse, Polygons,
-                        ErrorBars, Text, HLine, VLine, Spline,
+                        ErrorBars, Text, HLine, VLine, Spline, Spikes,
                         Table, ItemTable, Surface, Scatter3D, Trisurface)
 from ...core.options import Options, Cycle, OptionTree
 from ...interface import DFrame
@@ -14,7 +14,7 @@
 from .callbacks import Callbacks
 from .element import OverlayPlot, BokehMPLWrapper, BokehMPLRawWrapper
 from .chart import (PointPlot, CurvePlot, SpreadPlot, ErrorPlot, HistogramPlot,
-                    AdjointHistogramPlot)
+                    AdjointHistogramPlot, SpikesPlot)
 from .path import PathPlot, PolygonPlot
 from .plot import GridPlot, LayoutPlot, AdjointLayoutPlot
 from .raster import RasterPlot, RGBPlot, HeatmapPlot
@@ -37,6 +37,7 @@
                 Scatter: PointPlot,
                 ErrorBars: ErrorPlot,
                 Spread: SpreadPlot,
+                Spikes: SpikesPlot,
 
                 # Rasters
                 Image: RasterPlot,
@@ -81,7 +82,7 @@
 
 
 AdjointLayoutPlot.registry[Histogram] = AdjointHistogramPlot
-
+AdjointLayoutPlot.registry[Spikes] = Spikes
 
 try:
     from ..mpl.seaborn import TimeSeriesPlot, BivariatePlot, DistributionPlot
diff --git a/holoviews/plotting/bokeh/chart.py b/holoviews/plotting/bokeh/chart.py
index 2d22abf261..4d55bb3b55 100644
--- a/holoviews/plotting/bokeh/chart.py
+++ b/holoviews/plotting/bokeh/chart.py
@@ -203,3 +203,53 @@ def get_data(self, element, ranges=None):
                 err_xs.append((x, x))
                 err_ys.append((y - neg, y + pos))
         return (dict(xs=err_xs, ys=err_ys), self._mapping)
+
+
+class SpikesPlot(PathPlot):
+
+    color_index = param.Integer(default=1, doc="""
+      Index of the dimension from which the color will the drawn""")
+
+    spike_height = param.Number(default=0.1)
+
+    yposition = param.Number(default=0.)
+
+    style_opts = (['cmap', 'palette'] + line_properties)
+
+    def get_extents(self, element, ranges):
+        l, b, r, t = super(SpikesPlot, self).get_extents(element, ranges)
+        if len(element.dimensions()) == 1:
+            b, t = self.yposition, self.yposition+self.spike_height
+        return l, b, r, t
+
+
+    def get_data(self, element, ranges=None):
+        style = self.style[self.cyclic_index]
+        dims = element.dimensions(label=True)
+
+        ypos = self.yposition
+        if len(dims) > 1:
+            xs, ys = zip(*(((x, x), (ypos, ypos+y))
+                           for x, y in element.array()))
+            mapping = dict(xs=dims[0], ys=dims[1])
+            keys = (dims[0], dims[1])
+        else:
+            height = self.spike_height
+            xs, ys = zip(*(((x[0], x[0]), (ypos, ypos+height))
+                           for x in element.array()))
+            mapping = dict(xs=dims[0], ys='heights')
+            keys = (dims[0], 'heights')
+        if self.invert_axes: keys = keys[::-1]
+        data = dict(zip(keys, (xs, ys)))
+
+        cmap = style.get('palette', style.get('cmap', None))        
+        if self.color_index < len(dims) and cmap:
+            cdim = dims[self.color_index]
+            map_key = 'color_' + cdim
+            mapping['color'] = map_key
+            cmap = get_cmap(cmap)
+            colors = element.dimension_values(cdim)
+            crange = ranges.get(cdim, None)
+            data[map_key] = map_colors(colors, crange, cmap)
+
+        return data, mapping
diff --git a/holoviews/plotting/mpl/__init__.py b/holoviews/plotting/mpl/__init__.py
index 2e6c8ccf6d..1a1768f261 100644
--- a/holoviews/plotting/mpl/__init__.py
+++ b/holoviews/plotting/mpl/__init__.py
@@ -108,6 +108,7 @@ def grid_selector(grid):
                 VectorField: VectorFieldPlot,
                 ErrorBars: ErrorPlot,
                 Spread: SpreadPlot,
+                Spikes: SpikesPlot,
 
                 # General plots
                 GridSpace: GridPlot,
@@ -157,7 +158,8 @@ def grid_selector(grid):
 
 
 MPLPlot.sideplots.update({Histogram: SideHistogramPlot,
-                          GridSpace: GridPlot})
+                          GridSpace: GridPlot,
+                          Spikes: MarginalRugPlot})
 
 options = Store.options(backend='matplotlib')
 
diff --git a/holoviews/plotting/mpl/chart.py b/holoviews/plotting/mpl/chart.py
index c9612727a5..4db6d40601 100644
--- a/holoviews/plotting/mpl/chart.py
+++ b/holoviews/plotting/mpl/chart.py
@@ -4,6 +4,7 @@
 import numpy as np
 from matplotlib import cm
 from matplotlib import pyplot as plt
+from matplotlib.collections import LineCollection
 
 import param
 
@@ -12,6 +13,7 @@
 from ...element import Points, Raster, Polygons
 from ..util import compute_sizes, get_sideplot_ranges
 from .element import ElementPlot, ColorbarPlot, LegendPlot
+from .path  import PathPlot
 
 
 class ChartPlot(ElementPlot):
@@ -970,3 +972,105 @@ def update_handles(self, axis, element, key, ranges=None):
                         bar[0].set_height(height)
                         bar[0].set_y(prev)
                         prev += height if np.isfinite(height) else 0
+
+
+class SpikesPlot(PathPlot):
+
+    aspect = param.Parameter(default='square', doc="""
+        The aspect ratio mode of the plot. Allows setting an
+        explicit aspect ratio as width/height as well as
+        'square' and 'equal' options.""")
+
+    color_index = param.Integer(default=1, doc="""
+      Index of the dimension from which the color will the drawn""")
+
+    spike_height = param.Number(default=0.5)
+
+    yposition = param.Number(default=0)
+
+    style_opts = PathPlot.style_opts + ['cmap']
+
+    def initialize_plot(self, ranges=None):
+        lines = self.hmap.last
+        key = self.keys[-1]
+
+        ranges = self.compute_ranges(self.hmap, key, ranges)
+        ranges = match_spec(lines, ranges)
+        style = self.style[self.cyclic_index]
+        label = lines.label if self.show_legend else ''
+
+        data, array, clim = self.get_data(lines, ranges)
+        if array is not None:
+            style['array'] = array
+            style['clim'] = clim
+
+        line_segments = LineCollection(data, label=label,
+                                       zorder=self.zorder, **style)
+        self.handles['artist'] = line_segments
+        self.handles['axis'].add_collection(line_segments)
+
+        return self._finalize_axis(key, ranges=ranges)
+
+
+    def get_data(self, element, ranges):
+        dimensions = element.dimensions(label=True)
+        ndims = len(dimensions)
+
+        ypos = self.yposition
+        if ndims > 1:
+            data = [[(x, ypos), (x, ypos+y)] for x, y in element.array()]
+        else:
+            height = self.spike_height
+            data = [[(x[0], ypos), (x[0], ypos+height)] for x in element.array()]
+
+        if self.invert_axes:
+            data = [(line[0][::-1], line[1][::-1]) for line in data]
+
+        array, clim = None, None
+        if self.color_index < ndims:
+            cdim = dimensions[self.color_index]
+            array = element.dimension_values(cdim)
+            clime = ranges[cdim]
+        return data, array, clim
+
+
+    def update_handles(self, axis, element, key, ranges=None):
+        artist = self.handles['artist']
+        data, array, clim = self.get_data(element)
+        artist.set_paths(data)
+        visible = self.style[self.cyclic_index].get('visible', True)
+        artist.set_visible(visible)
+        if array is not None:
+            paths.set_clim(ranges[val_dim])
+            paths.set_array(cs)
+
+
+class MarginalRugPlot(SpikesPlot):
+
+    aspect = param.Parameter(default='auto', doc="""
+        Aspect ratios on SideHistogramPlot should be determined by the
+        AdjointLayoutPlot.""")
+
+    show_title = param.Boolean(default=False, doc="""
+        Titles should be disabled on all SidePlots to avoid clutter.""")
+
+    show_frame = param.Boolean(default=False)
+
+    show_xlabel = param.Boolean(default=False, doc="""
+        Whether to show the x-label of the plot. Disabled by default
+        because plots are often too cramped to fit the title correctly.""")
+
+    xaxis = param.ObjectSelector(default='bare',
+                                 objects=['top', 'bottom', 'bare', 'top-bare',
+                                          'bottom-bare', None], doc="""
+        Whether and where to display the xaxis, bare options allow suppressing
+        all axis labels including ticks and xlabel. Valid options are 'top',
+        'bottom', 'bare', 'top-bare' and 'bottom-bare'.""")
+
+    yaxis = param.ObjectSelector(default='bare',
+                                      objects=['left', 'right', 'bare', 'left-bare',
+                                               'right-bare', None], doc="""
+        Whether and where to display the yaxis, bare options allow suppressing
+        all axis labels including ticks and ylabel. Valid options are 'left',
+        'right', 'bare' 'left-bare' and 'right-bare'.""")
+

From 2d4105d0612a9d8db5b372e3ec88566e5384637d Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Thu, 10 Dec 2015 17:47:18 +0000
Subject: [PATCH 04/16] Added Spikes Element examples to Tutorial

---
 doc/Tutorials/Elements.ipynb | 90 ++++++++++++++++++++++++++++++++++++
 1 file changed, 90 insertions(+)

diff --git a/doc/Tutorials/Elements.ipynb b/doc/Tutorials/Elements.ipynb
index a6d17f0bd6..3a3965a95c 100644
--- a/doc/Tutorials/Elements.ipynb
+++ b/doc/Tutorials/Elements.ipynb
@@ -33,6 +33,7 @@
     "  <dt>[``Scatter``](#Scatter)</dt><dd>Discontinuous collection of points indexed over a single dimension.</dd>\n",
     "  <dt>[``Points``](#Points)</dt><dd>Discontinuous collection of points indexed over two dimensions.</dd>\n",
     "  <dt>[``VectorField``](#VectorField)</dt><dd>Cyclic variable (and optional auxiliary data) distributed over two-dimensional space.</dd>\n",
+    "  <dt>[``Spikes``](#Spikes)</dt><dd>A collection of horizontal or vertical lines at various locations with fixed height (1D) or variable height (2D).</dd>\n",
     "  <dt>[``SideHistogram``](#SideHistogram)</dt><dd>Histogram binning data contained by some other ``Element``.</dd>\n",
     "  </dl>\n",
     "\n",
@@ -461,6 +462,95 @@
     "points + points[0.3:0.7, 0.3:0.7].hist()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### ``Spikes`` <a id='Spikes'></a>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Spikes represent any number of horizontal or vertical line segments with fixed or variable heights. There are a number of uses for this type, first of all they may be used as a rugplot to give an overview of a one-dimensional distribution. They may also be useful in more domain specific cases, such as visualizing spike trains for neurophysiology or spectrograms in physics and chemistry applications.\n",
+    "\n",
+    "In the simplest case a Spikes object therefore represents a 1D distribution:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "%%opts Spikes [spike_height=0.1] (alpha=0.4)\n",
+    "xs = np.random.rand(50)\n",
+    "ys = np.random.rand(50)\n",
+    "hv.Points((xs, ys)) * hv.Spikes(xs)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "When supplying two dimensions to the Spikes object the second dimension will be mapped onto the line height. Optionally you may also supply a cmap and color_index to map color onto one of the dimensions. This way we can for example plot a mass spectrogram:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "%%opts Spikes (cmap='Blues')\n",
+    "hv.Spikes(np.random.rand(20, 2), kdims=['Mass'], vdims=['Intensity'])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Another possibility is to draw a number of spike trains as you would encounter in neuroscience:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "%%opts Spikes [spike_height=0.1] NdOverlay [show_legend=False]\n",
+    "hv.NdOverlay({i: hv.Spikes(np.random.rand(10, 1))(plot=dict(yposition=0.1*i))\n",
+    "              for i in range(10)})(plot=dict(yticks=[((i+1)*0.1-0.05, i)for i in range(10)]))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Finally we may use ``Spikes`` to adjoin to a regular plot to visualize marginal distributions:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "%%opts Spikes (alpha=0.4) [bgcolor='w'] AdjointLayout [border_size=0]\n",
+    "points = hv.Points(np.random.randn(100, 2))\n",
+    "points << hv.Spikes(points['y']) << hv.Spikes(points['x'])"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

From 45b542f7e865511026e539053ed4f9f169d1bb94 Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Thu, 10 Dec 2015 18:01:12 +0000
Subject: [PATCH 05/16] Minor fixes in bokeh plotting

---
 holoviews/plotting/bokeh/__init__.py | 2 +-
 holoviews/plotting/bokeh/element.py  | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/holoviews/plotting/bokeh/__init__.py b/holoviews/plotting/bokeh/__init__.py
index c1978d4e16..5a8cb47d1d 100644
--- a/holoviews/plotting/bokeh/__init__.py
+++ b/holoviews/plotting/bokeh/__init__.py
@@ -82,7 +82,7 @@
 
 
 AdjointLayoutPlot.registry[Histogram] = AdjointHistogramPlot
-AdjointLayoutPlot.registry[Spikes] = Spikes
+AdjointLayoutPlot.registry[Spikes] = SpikesPlot
 
 try:
     from ..mpl.seaborn import TimeSeriesPlot, BivariatePlot, DistributionPlot
diff --git a/holoviews/plotting/bokeh/element.py b/holoviews/plotting/bokeh/element.py
index f5d9166657..48dd3b90b5 100644
--- a/holoviews/plotting/bokeh/element.py
+++ b/holoviews/plotting/bokeh/element.py
@@ -140,8 +140,7 @@ class ElementPlot(BokehPlot, GenericElementPlot):
     # instance attribute.
     _update_handles = ['source', 'glyph']
 
-    def __init__(self, element, plot=None, invert_axes=False,
-                 show_labels=['x', 'y'], **params):
+    def __init__(self, element, plot=None, show_labels=['x', 'y'], **params):
         self.show_labels = show_labels
         self.current_ranges = None
         super(ElementPlot, self).__init__(element, **params)

From 8f38f3c350e6e293697f9372d9cf4003953a273f Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Fri, 11 Dec 2015 02:18:26 +0000
Subject: [PATCH 06/16] Renamed SpikesPlot plot options

---
 holoviews/plotting/bokeh/chart.py | 19 +++++++++++--------
 holoviews/plotting/mpl/chart.py   | 14 ++++++++------
 2 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/holoviews/plotting/bokeh/chart.py b/holoviews/plotting/bokeh/chart.py
index 4d55bb3b55..5c5c634a62 100644
--- a/holoviews/plotting/bokeh/chart.py
+++ b/holoviews/plotting/bokeh/chart.py
@@ -210,16 +210,18 @@ class SpikesPlot(PathPlot):
     color_index = param.Integer(default=1, doc="""
       Index of the dimension from which the color will the drawn""")
 
-    spike_height = param.Number(default=0.1)
+    spike_length = param.Number(default=0.5, doc="""
+      The length of each spike if Spikes object is one dimensional.""")
 
-    yposition = param.Number(default=0.)
+    position = param.Number(default=0., doc="""
+      The position of the lower end of each spike.""")
 
-    style_opts = (['cmap', 'palette'] + line_properties)
+    style_opts = (['color', 'cmap', 'palette'] + line_properties)
 
     def get_extents(self, element, ranges):
         l, b, r, t = super(SpikesPlot, self).get_extents(element, ranges)
         if len(element.dimensions()) == 1:
-            b, t = self.yposition, self.yposition+self.spike_height
+            b, t = self.position, self.position+self.spike_length
         return l, b, r, t
 
 
@@ -227,18 +229,19 @@ def get_data(self, element, ranges=None):
         style = self.style[self.cyclic_index]
         dims = element.dimensions(label=True)
 
-        ypos = self.yposition
+        pos = self.position
         if len(dims) > 1:
-            xs, ys = zip(*(((x, x), (ypos, ypos+y))
+            xs, ys = zip(*(((x, x), (pos, pos+y))
                            for x, y in element.array()))
             mapping = dict(xs=dims[0], ys=dims[1])
             keys = (dims[0], dims[1])
         else:
-            height = self.spike_height
-            xs, ys = zip(*(((x[0], x[0]), (ypos, ypos+height))
+            height = self.spike_length
+            xs, ys = zip(*(((x[0], x[0]), (pos, pos+height))
                            for x in element.array()))
             mapping = dict(xs=dims[0], ys='heights')
             keys = (dims[0], 'heights')
+
         if self.invert_axes: keys = keys[::-1]
         data = dict(zip(keys, (xs, ys)))
 
diff --git a/holoviews/plotting/mpl/chart.py b/holoviews/plotting/mpl/chart.py
index 4db6d40601..b6082029ee 100644
--- a/holoviews/plotting/mpl/chart.py
+++ b/holoviews/plotting/mpl/chart.py
@@ -984,9 +984,11 @@ class SpikesPlot(PathPlot):
     color_index = param.Integer(default=1, doc="""
       Index of the dimension from which the color will the drawn""")
 
-    spike_height = param.Number(default=0.5)
+    spike_length = param.Number(default=0.5, doc="""
+      The length of each spike if Spikes object is one dimensional.""")
 
-    yposition = param.Number(default=0)
+    position = param.Number(default=0., doc="""
+      The position of the lower end of each spike.""")
 
     style_opts = PathPlot.style_opts + ['cmap']
 
@@ -1016,12 +1018,12 @@ def get_data(self, element, ranges):
         dimensions = element.dimensions(label=True)
         ndims = len(dimensions)
 
-        ypos = self.yposition
+        ypos = self.position
         if ndims > 1:
-            data = [[(x, ypos), (x, ypos+y)] for x, y in element.array()]
+            data = [[(x, pos), (x, pos+y)] for x, y in element.array()]
         else:
-            height = self.spike_height
-            data = [[(x[0], ypos), (x[0], ypos+height)] for x in element.array()]
+            height = self.spike_length
+            data = [[(x[0], pos), (x[0], pos+height)] for x in element.array()]
 
         if self.invert_axes:
             data = [(line[0][::-1], line[1][::-1]) for line in data]

From 45f48196419d99649a89fa8af492c5aef84acc1f Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Fri, 11 Dec 2015 02:19:07 +0000
Subject: [PATCH 07/16] Improved default options for adjoined plots in bokeh

---
 holoviews/plotting/bokeh/chart.py | 12 +++++++++---
 holoviews/plotting/bokeh/plot.py  | 14 ++++++++------
 2 files changed, 17 insertions(+), 9 deletions(-)

diff --git a/holoviews/plotting/bokeh/chart.py b/holoviews/plotting/bokeh/chart.py
index 5c5c634a62..980741b686 100644
--- a/holoviews/plotting/bokeh/chart.py
+++ b/holoviews/plotting/bokeh/chart.py
@@ -4,7 +4,7 @@
 
 from ...core import Dimension
 from ...core.util import max_range
-from ...element import Chart, Raster, Points, Polygons
+from ...element import Chart, Raster, Points, Polygons, Spikes
 from ..util import compute_sizes, get_sideplot_ranges
 from .element import ElementPlot, line_properties, fill_properties
 from .path import PathPlot, PolygonPlot
@@ -147,13 +147,19 @@ class AdjointHistogramPlot(HistogramPlot):
 
     style_opts = HistogramPlot.style_opts + ['cmap']
 
-    width = param.Integer(default=125)
+    height = param.Integer(default=125, doc="The height of the plot")
+
+    width = param.Integer(default=125, doc="The width of the plot")
+
+    show_title = param.Boolean(default=False, doc="""
+        Whether to display the plot title.""")
 
     def get_data(self, element, ranges=None):
         if self.invert_axes:
             mapping = dict(top='left', bottom='right', left=0, right='top')
         else:
             mapping = dict(top='top', bottom=0, left='left', right='right')
+
         data = dict(top=element.values, left=element.edges[:-1],
                     right=element.edges[1:])
 
@@ -161,7 +167,7 @@ def get_data(self, element, ranges=None):
         main = self.adjoined.main
         range_item, main_range, dim = get_sideplot_ranges(self, element, main, ranges)
         vals = element.dimension_values(dim)
-        if isinstance(range_item, (Raster, Points, Polygons)):
+        if isinstance(range_item, (Raster, Points, Polygons, Spikes)):
             style = self.lookup_options(range_item, 'style')[self.cyclic_index]
         else:
             style = {}
diff --git a/holoviews/plotting/bokeh/plot.py b/holoviews/plotting/bokeh/plot.py
index dd04e3893b..fae3328145 100644
--- a/holoviews/plotting/bokeh/plot.py
+++ b/holoviews/plotting/bokeh/plot.py
@@ -353,13 +353,15 @@ def _create_subplots(self, layout, positions, layout_dimensions, ranges, num=0):
             if pos != 'main':
                 plot_type = AdjointLayoutPlot.registry.get(vtype, plot_type)
                 if pos == 'right':
-                    side_opts = dict(height=main_plot.height, yaxis='right',
-                                     invert_axes=True, width=120, show_labels=['y'],
-                                     xticks=2, show_title=False)
+                    yaxis = 'right-bare' if 'bare' in plot_type.yaxis else 'right'
+                    side_opts = dict(height=main_plot.height, yaxis=yaxis,
+                                     width=plot_type.width, invert_axes=True,
+                                     show_labels=['y'], xticks=1, xaxis=main_plot.xaxis)
                 else:
-                    side_opts = dict(width=main_plot.width, xaxis='top',
-                                     height=120, show_labels=['x'], yticks=2,
-                                     show_title=False)
+                    xaxis = 'top-bare' if 'bare' in plot_type.xaxis else 'top'
+                    side_opts = dict(width=main_plot.width, xaxis=xaxis,
+                                     height=plot_type.height, show_labels=['x'],
+                                     yticks=1, yaxis=main_plot.yaxis)
 
             # Override the plotopts as required
             # Customize plotopts depending on position.

From 588ae8a740a7dbf333fbbfee221e924ded0157c2 Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Fri, 11 Dec 2015 02:19:59 +0000
Subject: [PATCH 08/16] Added a MarginalSpikesPlot class for adjoined Spikes in
 bokeh

---
 holoviews/plotting/bokeh/__init__.py |  4 ++--
 holoviews/plotting/bokeh/chart.py    | 25 +++++++++++++++++++++++++
 2 files changed, 27 insertions(+), 2 deletions(-)

diff --git a/holoviews/plotting/bokeh/__init__.py b/holoviews/plotting/bokeh/__init__.py
index 5a8cb47d1d..600f43b220 100644
--- a/holoviews/plotting/bokeh/__init__.py
+++ b/holoviews/plotting/bokeh/__init__.py
@@ -14,7 +14,7 @@
 from .callbacks import Callbacks
 from .element import OverlayPlot, BokehMPLWrapper, BokehMPLRawWrapper
 from .chart import (PointPlot, CurvePlot, SpreadPlot, ErrorPlot, HistogramPlot,
-                    AdjointHistogramPlot, SpikesPlot)
+                    AdjointHistogramPlot, SpikesPlot, MarginalSpikesPlot)
 from .path import PathPlot, PolygonPlot
 from .plot import GridPlot, LayoutPlot, AdjointLayoutPlot
 from .raster import RasterPlot, RGBPlot, HeatmapPlot
@@ -82,7 +82,7 @@
 
 
 AdjointLayoutPlot.registry[Histogram] = AdjointHistogramPlot
-AdjointLayoutPlot.registry[Spikes] = SpikesPlot
+AdjointLayoutPlot.registry[Spikes] = MarginalSpikesPlot
 
 try:
     from ..mpl.seaborn import TimeSeriesPlot, BivariatePlot, DistributionPlot
diff --git a/holoviews/plotting/bokeh/chart.py b/holoviews/plotting/bokeh/chart.py
index 980741b686..b2350b7f6c 100644
--- a/holoviews/plotting/bokeh/chart.py
+++ b/holoviews/plotting/bokeh/chart.py
@@ -262,3 +262,28 @@ def get_data(self, element, ranges=None):
             data[map_key] = map_colors(colors, crange, cmap)
 
         return data, mapping
+
+
+
+class MarginalSpikesPlot(SpikesPlot):
+    """
+    SpikesPlot with useful defaults for plotting adjoined rug plot.
+    """
+
+    xaxis = param.ObjectSelector(default='top-bare',
+                                 objects=['top', 'bottom', 'bare', 'top-bare',
+                                          'bottom-bare', None], doc="""
+        Whether and where to display the xaxis, bare options allow suppressing
+        all axis labels including ticks and xlabel. Valid options are 'top',
+        'bottom', 'bare', 'top-bare' and 'bottom-bare'.""")
+
+    yaxis = param.ObjectSelector(default='right-bare',
+                                      objects=['left', 'right', 'bare', 'left-bare',
+                                               'right-bare', None], doc="""
+        Whether and where to display the yaxis, bare options allow suppressing
+        all axis labels including ticks and ylabel. Valid options are 'left',
+        'right', 'bare' 'left-bare' and 'right-bare'.""")
+
+    height = param.Integer(default=80, doc="Height of plot")
+
+    width = param.Integer(default=80, doc="Width of plot")

From 96daeb455b6005807ff92179f9b16955ad144da4 Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Fri, 11 Dec 2015 02:23:12 +0000
Subject: [PATCH 09/16] Fixed bug in mplt SpikesPlot

---
 holoviews/plotting/mpl/chart.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/holoviews/plotting/mpl/chart.py b/holoviews/plotting/mpl/chart.py
index b6082029ee..3af3bdd4c2 100644
--- a/holoviews/plotting/mpl/chart.py
+++ b/holoviews/plotting/mpl/chart.py
@@ -1018,7 +1018,7 @@ def get_data(self, element, ranges):
         dimensions = element.dimensions(label=True)
         ndims = len(dimensions)
 
-        ypos = self.position
+        pos = self.position
         if ndims > 1:
             data = [[(x, pos), (x, pos+y)] for x, y in element.array()]
         else:

From 4345ea13696311578797641dfb99f91c8abc835e Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Fri, 11 Dec 2015 02:41:10 +0000
Subject: [PATCH 10/16] Changed Spikes styling details

---
 holoviews/plotting/bokeh/__init__.py | 1 +
 holoviews/plotting/mpl/__init__.py   | 1 +
 holoviews/plotting/mpl/chart.py      | 5 ++++-
 3 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/holoviews/plotting/bokeh/__init__.py b/holoviews/plotting/bokeh/__init__.py
index 600f43b220..136e2e6ddb 100644
--- a/holoviews/plotting/bokeh/__init__.py
+++ b/holoviews/plotting/bokeh/__init__.py
@@ -115,6 +115,7 @@
 options.Spread = Options('style', fill_color=Cycle(), fill_alpha=0.6, line_color='black')
 options.Histogram = Options('style', fill_color="#036564", line_color="#033649")
 options.Points = Options('style', color=Cycle())
+options.Spikes = Options('style', color='black')
 
 # Paths
 options.Contours = Options('style', color=Cycle())
diff --git a/holoviews/plotting/mpl/__init__.py b/holoviews/plotting/mpl/__init__.py
index 1a1768f261..1fd5d3c228 100644
--- a/holoviews/plotting/mpl/__init__.py
+++ b/holoviews/plotting/mpl/__init__.py
@@ -177,6 +177,7 @@ def grid_selector(grid):
 options.Scatter3D = Options('style', facecolors=Cycle(), marker='o')
 options.Scatter3D = Options('plot', fig_size=150)
 options.Surface = Options('plot', fig_size=150)
+options.Spikes = Options('style', color='black')
 # Rasters
 options.Image = Options('style', cmap='hot', interpolation='nearest')
 options.Raster = Options('style', cmap='hot', interpolation='nearest')
diff --git a/holoviews/plotting/mpl/chart.py b/holoviews/plotting/mpl/chart.py
index 3af3bdd4c2..bb3fc23d90 100644
--- a/holoviews/plotting/mpl/chart.py
+++ b/holoviews/plotting/mpl/chart.py
@@ -984,7 +984,7 @@ class SpikesPlot(PathPlot):
     color_index = param.Integer(default=1, doc="""
       Index of the dimension from which the color will the drawn""")
 
-    spike_length = param.Number(default=0.5, doc="""
+    spike_length = param.Number(default=0.1, doc="""
       The length of each spike if Spikes object is one dimensional.""")
 
     position = param.Number(default=0., doc="""
@@ -1053,6 +1053,9 @@ class MarginalRugPlot(SpikesPlot):
         Aspect ratios on SideHistogramPlot should be determined by the
         AdjointLayoutPlot.""")
 
+    bgcolor = param.Parameter(default=(1, 1, 1, 0), doc="""
+        Make plot background invisible.""")
+
     show_title = param.Boolean(default=False, doc="""
         Titles should be disabled on all SidePlots to avoid clutter.""")
 

From 1c047bb5934a654f78062b77cd88da30722a95e5 Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Fri, 11 Dec 2015 02:52:48 +0000
Subject: [PATCH 11/16] Updated Spikes examples in notebooks

---
 doc/Tutorials/Elements.ipynb | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/doc/Tutorials/Elements.ipynb b/doc/Tutorials/Elements.ipynb
index 3a3965a95c..66f14e9995 100644
--- a/doc/Tutorials/Elements.ipynb
+++ b/doc/Tutorials/Elements.ipynb
@@ -486,7 +486,7 @@
    },
    "outputs": [],
    "source": [
-    "%%opts Spikes [spike_height=0.1] (alpha=0.4)\n",
+    "%%opts Spikes (alpha=0.4)\n",
     "xs = np.random.rand(50)\n",
     "ys = np.random.rand(50)\n",
     "hv.Points((xs, ys)) * hv.Spikes(xs)"
@@ -507,7 +507,7 @@
    },
    "outputs": [],
    "source": [
-    "%%opts Spikes (cmap='Blues')\n",
+    "%%opts Spikes (cmap='Reds')\n",
     "hv.Spikes(np.random.rand(20, 2), kdims=['Mass'], vdims=['Intensity'])"
    ]
   },
@@ -515,7 +515,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Another possibility is to draw a number of spike trains as you would encounter in neuroscience:"
+    "Another possibility is to draw a number of spike trains as you would encounter in neuroscience. Here we generate 10 separate random spike trains and distribute them evenly across the space by setting their ``position``. By also declaring some yticks each spike traing can be labeled individually:"
    ]
   },
   {
@@ -526,16 +526,16 @@
    },
    "outputs": [],
    "source": [
-    "%%opts Spikes [spike_height=0.1] NdOverlay [show_legend=False]\n",
-    "hv.NdOverlay({i: hv.Spikes(np.random.rand(10, 1))(plot=dict(yposition=0.1*i))\n",
-    "              for i in range(10)})(plot=dict(yticks=[((i+1)*0.1-0.05, i)for i in range(10)]))"
+    "%%opts Spikes NdOverlay [show_legend=False]\n",
+    "hv.NdOverlay({i: hv.Spikes(np.random.randint(0, 100, 10), kdims=['Time'])(plot=dict(position=0.1*i))\n",
+    "              for i in range(10)})(plot=dict(yticks=[((i+1)*0.1-0.05, i) for i in range(10)]))"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Finally we may use ``Spikes`` to adjoin to a regular plot to visualize marginal distributions:"
+    "Finally we may use ``Spikes`` to visualize marginal distributions as adjoined plots:"
    ]
   },
   {
@@ -546,8 +546,8 @@
    },
    "outputs": [],
    "source": [
-    "%%opts Spikes (alpha=0.4) [bgcolor='w'] AdjointLayout [border_size=0]\n",
-    "points = hv.Points(np.random.randn(100, 2))\n",
+    "%%opts Spikes (alpha=0.05) [spike_length=0.5] AdjointLayout [border_size=0]\n",
+    "points = hv.Points(np.random.randn(500, 2))\n",
     "points << hv.Spikes(points['y']) << hv.Spikes(points['x'])"
    ]
   },

From 9e3e44e28bcbb0f3026eaec225ebcc44e566644e Mon Sep 17 00:00:00 2001
From: philippjfr <P.Rudiger@ed.ac.uk>
Date: Fri, 11 Dec 2015 14:30:41 +0000
Subject: [PATCH 12/16] Updated reference_data submodule reference

---
 doc/reference_data | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/reference_data b/doc/reference_data
index 0391727272..860116e0fb 160000
--- a/doc/reference_data
+++ b/doc/reference_data
@@ -1 +1 @@
-Subproject commit 0391727272a64381496f8a62b591672c3fb8f2c1
+Subproject commit 860116e0fb8744d85a90d88d0a6ec5d35da814e1

From 6c7c9f5cea30b6eed6d1bf33ee1322366fe4b328 Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Fri, 11 Dec 2015 14:40:12 +0000
Subject: [PATCH 13/16] Added Spikes Element comparison

---
 holoviews/element/comparison.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/holoviews/element/comparison.py b/holoviews/element/comparison.py
index 7bf3aaee0e..56c5046389 100644
--- a/holoviews/element/comparison.py
+++ b/holoviews/element/comparison.py
@@ -154,6 +154,7 @@ def register(cls):
         cls.equality_type_funcs[Trisurface] =   cls.compare_trisurface
         cls.equality_type_funcs[Histogram] =    cls.compare_histogram
         cls.equality_type_funcs[Bars] =         cls.compare_bars
+        cls.equality_type_funcs[Spikes] =       cls.compare_spikes
 
         # Tables
         cls.equality_type_funcs[ItemTable] =    cls.compare_itemtables
@@ -500,6 +501,10 @@ def compare_vectorfield(cls, el1, el2, msg='VectorField'):
     def compare_bars(cls, el1, el2, msg='Bars'):
         cls.compare_columns(el1, el2, msg)
 
+    @classmethod
+    def compare_spikes(cls, el1, el2, msg='Spikes'):
+        cls.compare_columns(el1, el2, msg)
+
     #=========#
     # Rasters #
     #=========#

From 527033ec583e907f5c275a30acf2bf49f3ab228c Mon Sep 17 00:00:00 2001
From: philippjfr <P.Rudiger@ed.ac.uk>
Date: Fri, 11 Dec 2015 15:25:23 +0000
Subject: [PATCH 14/16] Updated reference_data submodule reference

---
 doc/reference_data | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/reference_data b/doc/reference_data
index 860116e0fb..014c069ea2 160000
--- a/doc/reference_data
+++ b/doc/reference_data
@@ -1 +1 @@
-Subproject commit 860116e0fb8744d85a90d88d0a6ec5d35da814e1
+Subproject commit 014c069ea26ed90f289b0362577cdee2310b3618

From 95dbccd3a4e2e8e6442060f8bbb2ee5c633d1846 Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Fri, 11 Dec 2015 15:23:57 +0000
Subject: [PATCH 15/16] Updated Spikes docstring

---
 holoviews/element/chart.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/holoviews/element/chart.py b/holoviews/element/chart.py
index 5e5a01ab73..82f66a10a5 100644
--- a/holoviews/element/chart.py
+++ b/holoviews/element/chart.py
@@ -349,11 +349,12 @@ def __init__(self, data, **params):
 
 class Spikes(Chart):
     """
-    Spikes is a 1D or 2D Element, which represents vertical or
-    horizontal ticks along some dimension.  If an additional dimension
-    is supplied it will be used to specify the height of the
-    lines. The Element may therefore be used to represent 1D
-    distributions, spectrograms or spike trains in electrophysiology.
+    Spikes is a 1D or 2D Element, which represents a series of
+    vertical or horizontal lines distributed along some dimension. If
+    an additional dimension is supplied it will be used to specify the
+    height of the lines. The Element may therefore be used to
+    represent 1D distributions, spectrograms or spike trains in
+    electrophysiology.
     """
 
     group = param.String(default='Spikes', constant=True)

From 7716fba118d75eade861d2120c017bcb9ccf4b0d Mon Sep 17 00:00:00 2001
From: Philipp Rudiger <P.Rudiger@ed.ac.uk>
Date: Fri, 11 Dec 2015 16:03:32 +0000
Subject: [PATCH 16/16] Consistent naming for adjoined plots

---
 holoviews/plotting/bokeh/__init__.py | 6 +++---
 holoviews/plotting/bokeh/chart.py    | 4 ++--
 holoviews/plotting/mpl/__init__.py   | 2 +-
 holoviews/plotting/mpl/chart.py      | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/holoviews/plotting/bokeh/__init__.py b/holoviews/plotting/bokeh/__init__.py
index 136e2e6ddb..485294b374 100644
--- a/holoviews/plotting/bokeh/__init__.py
+++ b/holoviews/plotting/bokeh/__init__.py
@@ -14,7 +14,7 @@
 from .callbacks import Callbacks
 from .element import OverlayPlot, BokehMPLWrapper, BokehMPLRawWrapper
 from .chart import (PointPlot, CurvePlot, SpreadPlot, ErrorPlot, HistogramPlot,
-                    AdjointHistogramPlot, SpikesPlot, MarginalSpikesPlot)
+                    SideHistogramPlot, SpikesPlot, SideSpikesPlot)
 from .path import PathPlot, PolygonPlot
 from .plot import GridPlot, LayoutPlot, AdjointLayoutPlot
 from .raster import RasterPlot, RGBPlot, HeatmapPlot
@@ -81,8 +81,8 @@
                'bokeh')
 
 
-AdjointLayoutPlot.registry[Histogram] = AdjointHistogramPlot
-AdjointLayoutPlot.registry[Spikes] = MarginalSpikesPlot
+AdjointLayoutPlot.registry[Histogram] = SideHistogramPlot
+AdjointLayoutPlot.registry[Spikes] = SideSpikesPlot
 
 try:
     from ..mpl.seaborn import TimeSeriesPlot, BivariatePlot, DistributionPlot
diff --git a/holoviews/plotting/bokeh/chart.py b/holoviews/plotting/bokeh/chart.py
index b2350b7f6c..79f8ad16bf 100644
--- a/holoviews/plotting/bokeh/chart.py
+++ b/holoviews/plotting/bokeh/chart.py
@@ -143,7 +143,7 @@ def get_data(self, element, ranges=None):
         return (data, mapping)
 
 
-class AdjointHistogramPlot(HistogramPlot):
+class SideHistogramPlot(HistogramPlot):
 
     style_opts = HistogramPlot.style_opts + ['cmap']
 
@@ -265,7 +265,7 @@ def get_data(self, element, ranges=None):
 
 
 
-class MarginalSpikesPlot(SpikesPlot):
+class SideSpikesPlot(SpikesPlot):
     """
     SpikesPlot with useful defaults for plotting adjoined rug plot.
     """
diff --git a/holoviews/plotting/mpl/__init__.py b/holoviews/plotting/mpl/__init__.py
index 1fd5d3c228..e331ee7d56 100644
--- a/holoviews/plotting/mpl/__init__.py
+++ b/holoviews/plotting/mpl/__init__.py
@@ -159,7 +159,7 @@ def grid_selector(grid):
 
 MPLPlot.sideplots.update({Histogram: SideHistogramPlot,
                           GridSpace: GridPlot,
-                          Spikes: MarginalRugPlot})
+                          Spikes: SideSpikesPlot})
 
 options = Store.options(backend='matplotlib')
 
diff --git a/holoviews/plotting/mpl/chart.py b/holoviews/plotting/mpl/chart.py
index bb3fc23d90..4858ef159a 100644
--- a/holoviews/plotting/mpl/chart.py
+++ b/holoviews/plotting/mpl/chart.py
@@ -1047,7 +1047,7 @@ def update_handles(self, axis, element, key, ranges=None):
             paths.set_array(cs)
 
 
-class MarginalRugPlot(SpikesPlot):
+class SideSpikesPlot(SpikesPlot):
 
     aspect = param.Parameter(default='auto', doc="""
         Aspect ratios on SideHistogramPlot should be determined by the