hv_anndata.plotting.scanpy.scatter

hv_anndata.plotting.scanpy.scatter(adata, /, kdims, vdims=(), *, color=None)

Shortcut for a scatter plot.

Basically just

>>> hv.Scatter(adata, kdims[0], [kdims[1], *vdims]).opts(aspect="square", ...)

If color is set, it’s both added to vdims and in .opts(color=...).

Parameters:

adata AnnData

The AnnData object.

kdims Collection[AdDim]

A sequence containing the x and y dimension.

vdims Collection[AdDim], default: ()

The value dimensions (color will be added automatically).

color AdDim | None, default: None

The color dimension.

Return type:

Scatter

Returns:

A scatter plot object

Examples

bokeh

import hv_anndata.plotting.scanpy as hv_sc
from hv_anndata import data, register, A

register()

adata = data.pbmc68k_processed()
hv_sc.scatter(adata, A.X[:, ["PSAP", "C1QA"]], color=A.obs["bulk_labels"]).opts(
    cmap="tab10", show_legend=False
)

matplotlib

import hv_anndata.plotting.scanpy as hv_sc
from hv_anndata import data, register, A

register()

adata = data.pbmc68k_processed()
hv_sc.scatter(adata, A.X[:, ["PSAP", "C1QA"]], color=A.obs["bulk_labels"]).opts(
    cmap="tab10", show_legend=False
)

plotly

import hv_anndata.plotting.scanpy as hv_sc
from hv_anndata import data, register, A

register()

adata = data.pbmc68k_processed()
hv_sc.scatter(adata, A.X[:, ["PSAP", "C1QA"]], color=A.obs["bulk_labels"]).opts(
    cmap="tab10", show_legend=False
)

WARNING:param.main: Option 'legend_position' for Scatter type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh', 'matplotlib']

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1381, in Dimensioned._repr_mimebundle_(self, include, exclude)
   1374 def _repr_mimebundle_(self, include=None, exclude=None):
   1375     """Resolves the class hierarchy for the class rendering the
   1376     object using any display hooks registered on Store.display
   1377     hooks.  The output of all registered display_hooks is then
   1378     combined and returned.
   1379 
   1380     """
-> 1381     return Store.render(self)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/options.py:1433, in Store.render(cls, obj)
   1431 data, metadata = {}, {}
   1432 for hook in hooks:
-> 1433     ret = hook(obj)
   1434     if ret is None:
   1435         continue

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/ipython/display_hooks.py:340, in pprint_display(obj)
    338 if not ip.display_formatter.formatters['text/plain'].pprint:
    339     return None
--> 340 return display(obj, raw_output=True)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/ipython/display_hooks.py:308, in display(obj, raw_output, **kwargs)
    306 elif isinstance(obj, (CompositeOverlay, ViewableElement)):
    307     with option_state(obj):
--> 308         output = element_display(obj)
    309 elif isinstance(obj, (Layout, NdLayout, AdjointLayout)):
    310     with option_state(obj):

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/ipython/display_hooks.py:205, in display_hook.<locals>.wrapped(element)
    203 try:
    204     max_frames = OutputSettings.options['max_frames']
--> 205     mimebundle = fn(element, max_frames=max_frames)
    206     if mimebundle is None:
    207         return {}, {}

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/ipython/display_hooks.py:246, in element_display(element, max_frames)
    243 if type(element) not in Store.registry[backend]:
    244     return None
--> 246 return render(element)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/ipython/display_hooks.py:76, in render(obj, **kwargs)
     73 if renderer.fig == 'pdf':
     74     renderer = renderer.instance(fig='png')
---> 76 return renderer.components(obj, **kwargs)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/renderer.py:396, in Renderer.components(self, obj, fmt, comm, **kwargs)
    394 embed = (not (dynamic or streams or self.widget_mode == 'live') or config.embed)
    395 if embed or config.comms == 'default':
--> 396     return self._render_panel(plot, embed, comm)
    397 return self._render_ipywidget(plot)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/renderer.py:403, in Renderer._render_panel(self, plot, embed, comm)
    401 doc = Document()
    402 with config.set(embed=embed):
--> 403     model = plot.layout._render_model(doc, comm)
    404 if embed:
    405     return render_model(model, comm)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/panel/viewable.py:775, in Viewable._render_model(self, doc, comm)
    773 if comm is None:
    774     comm = state._comm_manager.get_server_comm()
--> 775 model = self.get_root(doc, comm)
    777 if self._design and self._design.theme.bokeh_theme:
    778     doc.theme = self._design.theme.bokeh_theme

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/panel/layout/base.py:332, in Panel.get_root(self, doc, comm, preprocess)
    328 def get_root(
    329     self, doc: Document | None = None, comm: Comm | None = None,
    330     preprocess: bool = True
    331 ) -> Model:
--> 332     root = super().get_root(doc, comm, preprocess)
    333     # ALERT: Find a better way to handle this
    334     if hasattr(root, 'styles') and 'overflow-x' in root.styles:

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/panel/viewable.py:705, in Renderable.get_root(self, doc, comm, preprocess)
    703 wrapper = self._design._wrapper(self)
    704 if wrapper is self:
--> 705     root = self._get_model(doc, comm=comm)
    706     if preprocess:
    707         self._preprocess(root)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/panel/layout/base.py:316, in Panel._get_model(self, doc, root, parent, comm)
    314 root = root or model
    315 self._models[root.ref['id']] = (model, parent)
--> 316 objects, _ = self._get_objects(model, [], doc, root, comm)
    317 props = self._get_properties(doc)
    318 props[self._property_mapping['objects']] = objects

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/panel/layout/base.py:298, in Panel._get_objects(self, model, old_objects, doc, root, comm)
    296 else:
    297     try:
--> 298         child = pane._get_model(doc, root, model, comm)
    299     except RerenderError as e:
    300         if e.layout is not None and e.layout is not self:

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/panel/pane/holoviews.py:498, in HoloViews._get_model(self, doc, root, parent, comm)
    496 plot.pane = self
    497 backend = plot.renderer.backend
--> 498 state = plot.renderer.get_plot_state(plot)
    500 # Ensure rerender if content is responsive but layout is centered
    501 # or update layout if plot is height responsive but layout wrapper
    502 # is not
    503 self._sync_sizing_mode(plot)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/plotly/renderer.py:86, in PlotlyRenderer.get_plot_state(self_or_cls, obj, doc, renderer, numpy_convert, **kwargs)
     82 clean_internal_figure_properties(fig_dict)
     84 # Run through Figure constructor to normalize keys
     85 # (e.g. to expand magic underscore notation)
---> 86 fig_dict = go.Figure(fig_dict).to_dict()
     87 fig_dict['config'] = config
     89 # Remove template

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/graph_objs/_figure.py:72, in Figure.__init__(self, data, layout, frames, skip_invalid, **kwargs)
     68         ValueError
     69             if a property in the specification of data, layout, or frames
     70             is invalid AND skip_invalid is False
     71         """
---> 72         super().__init__(data, layout, frames, skip_invalid, **kwargs)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/basedatatypes.py:532, in BaseFigure.__init__(self, data, layout_plotly, frames, skip_invalid, **kwargs)
    529 self._data_validator.set_uid = self._set_trace_uid
    531 # ### Import traces ###
--> 532 data = self._data_validator.validate_coerce(
    533     data, skip_invalid=skip_invalid, _validate=self._validate
    534 )
    536 # ### Save tuple of trace objects ###
    537 self._data_objs = data

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/_plotly_utils/basevalidators.py:2669, in BaseDataValidator.validate_coerce(self, v, skip_invalid, _validate)
   2667         invalid_els.append(v_el)
   2668 else:
-> 2669     trace = self.get_trace_class(trace_type)(
   2670         skip_invalid=skip_invalid, _validate=_validate, **v_el
   2671     )
   2672     res.append(trace)
   2674 if type_in_v_el:
   2675     # Restore type in v_el

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/graph_objs/_scatter.py:2797, in Scatter.__init__(self, arg, alignmentgroup, cliponaxis, connectgaps, customdata, customdatasrc, dx, dy, error_x, error_y, fill, fillcolor, fillgradient, fillpattern, groupnorm, hoverinfo, hoverinfosrc, hoverlabel, hoveron, hovertemplate, hovertemplatefallback, hovertemplatesrc, hovertext, hovertextsrc, ids, idssrc, legend, legendgroup, legendgrouptitle, legendrank, legendwidth, line, marker, meta, metasrc, mode, name, offsetgroup, opacity, orientation, selected, selectedpoints, showlegend, stackgaps, stackgroup, stream, text, textfont, textposition, textpositionsrc, textsrc, texttemplate, texttemplatefallback, texttemplatesrc, uid, uirevision, unselected, visible, x, x0, xaxis, xcalendar, xhoverformat, xperiod, xperiod0, xperiodalignment, xsrc, y, y0, yaxis, ycalendar, yhoverformat, yperiod, yperiod0, yperiodalignment, ysrc, zorder, **kwargs)
   2795 self._set_property("legendwidth", arg, legendwidth)
   2796 self._set_property("line", arg, line)
-> 2797 self._set_property("marker", arg, marker)
   2798 self._set_property("meta", arg, meta)
   2799 self._set_property("metasrc", arg, metasrc)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/basedatatypes.py:4403, in BasePlotlyType._set_property(self, name, arg, provided)
   4397 def _set_property(self, name, arg, provided):
   4398     """
   4399     Initialize a property of this object using the provided value
   4400     or a value popped from the arguments dictionary. If neither
   4401     is available, do not set the property.
   4402     """
-> 4403     _set_property_provided_value(self, name, arg, provided)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/basedatatypes.py:398, in _set_property_provided_value(obj, name, arg, provided)
    396 val = provided if provided is not None else val
    397 if val is not None:
--> 398     obj[name] = val

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/basedatatypes.py:4924, in BasePlotlyType.__setitem__(self, prop, value)
   4922 # ### Handle compound property ###
   4923 if isinstance(validator, CompoundValidator):
-> 4924     self._set_compound_prop(prop, value)
   4926 # ### Handle compound array property ###
   4927 elif isinstance(validator, (CompoundArrayValidator, BaseDataValidator)):

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/basedatatypes.py:5335, in BasePlotlyType._set_compound_prop(self, prop, val)
   5332 # Import value
   5333 # ------------
   5334 validator = self._get_validator(prop)
-> 5335 val = validator.validate_coerce(val, skip_invalid=self._skip_invalid)
   5337 # Save deep copies of current and new states
   5338 # ------------------------------------------
   5339 curr_val = self._compound_props.get(prop, None)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/_plotly_utils/basevalidators.py:2468, in CompoundValidator.validate_coerce(self, v, skip_invalid, _validate)
   2465     v = self.data_class()
   2467 elif isinstance(v, dict):
-> 2468     v = self.data_class(v, skip_invalid=skip_invalid, _validate=_validate)
   2470 elif isinstance(v, self.data_class):
   2471     # Copy object
   2472     v = self.data_class(v)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/graph_objs/scatter/_marker.py:1108, in Marker.__init__(self, arg, angle, angleref, anglesrc, autocolorscale, cauto, cmax, cmid, cmin, color, coloraxis, colorbar, colorscale, colorsrc, gradient, line, maxdisplayed, opacity, opacitysrc, reversescale, showscale, size, sizemin, sizemode, sizeref, sizesrc, standoff, standoffsrc, symbol, symbolsrc, **kwargs)
   1106 self._set_property("cmid", arg, cmid)
   1107 self._set_property("cmin", arg, cmin)
-> 1108 self._set_property("color", arg, color)
   1109 self._set_property("coloraxis", arg, coloraxis)
   1110 self._set_property("colorbar", arg, colorbar)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/basedatatypes.py:4403, in BasePlotlyType._set_property(self, name, arg, provided)
   4397 def _set_property(self, name, arg, provided):
   4398     """
   4399     Initialize a property of this object using the provided value
   4400     or a value popped from the arguments dictionary. If neither
   4401     is available, do not set the property.
   4402     """
-> 4403     _set_property_provided_value(self, name, arg, provided)

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/basedatatypes.py:398, in _set_property_provided_value(obj, name, arg, provided)
    396 val = provided if provided is not None else val
    397 if val is not None:
--> 398     obj[name] = val

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/basedatatypes.py:4932, in BasePlotlyType.__setitem__(self, prop, value)
   4928         self._set_array_prop(prop, value)
   4930     # ### Handle simple property ###
   4931     else:
-> 4932         self._set_prop(prop, value)
   4933 else:
   4934     # Make sure properties dict is initialized
   4935     self._init_props()

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/basedatatypes.py:5276, in BasePlotlyType._set_prop(self, prop, val)
   5274         return
   5275     else:
-> 5276         raise err
   5278 # val is None
   5279 # -----------
   5280 if val is None:
   5281     # Check if we should send null update

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/plotly/basedatatypes.py:5271, in BasePlotlyType._set_prop(self, prop, val)
   5268 validator = self._get_validator(prop)
   5270 try:
-> 5271     val = validator.validate_coerce(val)
   5272 except ValueError as err:
   5273     if self._skip_invalid:

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/_plotly_utils/basevalidators.py:1379, in ColorValidator.validate_coerce(self, v, should_raise)
   1376 invalid_els = self.find_invalid_els(v, validated_v)
   1378 if invalid_els and should_raise:
-> 1379     self.raise_invalid_elements(invalid_els)
   1381 # ### Check that elements have valid colors types ###
   1382 elif self.numbers_allowed() or invalid_els:

File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/_plotly_utils/basevalidators.py:328, in BaseValidator.raise_invalid_elements(self, invalid_els)
    326     def raise_invalid_elements(self, invalid_els):
    327         if invalid_els:
--> 328             raise ValueError(
    329                 """
    330     Invalid element(s) received for the '{name}' property of {pname}
    331         Invalid elements include: {invalid}
    332 
    333 {valid_clr_desc}""".format(
    334                     name=self.plotly_name,
    335                     pname=self.parent_name,
    336                     invalid=invalid_els[:10],
    337                     valid_clr_desc=self.description(),
    338                 )
    339             )

ValueError: 
    Invalid element(s) received for the 'color' property of scatter.marker
        Invalid elements include: ['CD14+ Monocyte', 'Dendritic', 'CD56+ NK', 'CD4+/CD25 T Reg', 'Dendritic', 'CD19+ B', 'Dendritic', 'Dendritic', 'CD8+ Cytotoxic T', 'CD14+ Monocyte']

    The 'color' property is a color and may be specified as:
      - A hex string (e.g. '#ff0000')
      - An rgb/rgba string (e.g. 'rgb(255,0,0)')
      - An hsl/hsla string (e.g. 'hsl(0,100%,50%)')
      - An hsv/hsva string (e.g. 'hsv(0,100%,100%)')
      - A named CSS color: see https://plotly.com/python/css-colors/ for a list
      - A number that will be interpreted as a color
        according to scatter.marker.colorscale
      - A list or array of any of the above

:Scatter   [A.X[:, 'PSAP']]   (C1QA,bulk_labels)