hv_anndata.plotting.scanpy.ranking¶
- hv_anndata.plotting.scanpy.ranking(adata, ref, /, n_points=10, *, include_lowest=True, label_dim=None)¶
Plot (e.g. PCA) score ranking.
- Parameters:
- adata
AnnData Annotated data matrix.
- ref
AdDim Dimension containing scores to rank.
- n_points
int, default:10 Number of points to plot.
- include_lowest
bool, default:True Whether to include the lowest-scored names in addition to the highest-scored ones.
- label_dim
AdDim|None, default:None Dimension to use for labels. The default is
dim’s axis index (e.g.A.obs.indexforA.obs["scores"]).
- adata
- Return type:
- Returns:
Holoviews plot with labels and points.
Examples
import hv_anndata.plotting.scanpy as hv_sc from hv_anndata import data, register, A register() adata = data.pbmc68k_processed() hv.Layout([ hv_sc.ranking(adata, A.varm["PCs"][0]).opts(aspect=1.2), hv_sc.ranking(adata, A.varm["PCs"][0], include_lowest=False).opts(aspect=0.6), ]).opts(shared_axes=False)
import hv_anndata.plotting.scanpy as hv_sc from hv_anndata import data, register, A register() adata = data.pbmc68k_processed() hv.Layout([ hv_sc.ranking(adata, A.varm["PCs"][0]).opts(aspect=1.2), hv_sc.ranking(adata, A.varm["PCs"][0], include_lowest=False).opts(aspect=0.6), ]).opts(shared_axes=False)
WARNING:param.main: Option 'angle' for Labels type not valid for selected backend ('matplotlib'). Option only applies to following backends: ['bokeh']WARNING:param.main: Option 'text_align' for Labels type not valid for selected backend ('matplotlib'). Option only applies to following backends: ['bokeh']WARNING:param.main: Option 'angle' for Labels type not valid for selected backend ('matplotlib'). Option only applies to following backends: ['bokeh']WARNING:param.main: Option 'text_align' for Labels type not valid for selected backend ('matplotlib'). Option only applies to following backends: ['bokeh']ValueError: Mapping a dimension to the "alpha" style option is not supported by the Points e ...
Traceback (most recent call last): File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/mpl/chart.py", line 605, in get_data style = self._apply_transforms(element, ranges, style) File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/mpl/element.py", line 723, in _apply_transforms raise ValueError(f'Mapping a dimension to the "{k}" ' ...<4 lines>... 'to overlay your data along the dimension.') ValueError: Mapping a dimension to the "alpha" style option is not supported by the Points element using the matplotlib backend. To map the "dot" dimension to the alpha use a groupby operation to overlay your data along the dimension.import hv_anndata.plotting.scanpy as hv_sc from hv_anndata import data, register, A register() adata = data.pbmc68k_processed() hv.Layout([ hv_sc.ranking(adata, A.varm["PCs"][0]).opts(aspect=1.2), hv_sc.ranking(adata, A.varm["PCs"][0], include_lowest=False).opts(aspect=0.6), ]).opts(shared_axes=False)
WARNING:param.main: Option 'angle' for Labels type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh']WARNING:param.main: Option 'text_align' for Labels type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh']WARNING:param.main: Option 'angle' for Labels type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh']WARNING:param.main: Option 'text_align' for Labels type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh']--------------------------------------------------------------------------- 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:311, in display(obj, raw_output, **kwargs) 309 elif isinstance(obj, (Layout, NdLayout, AdjointLayout)): 310 with option_state(obj): --> 311 output = layout_display(obj) 312 elif isinstance(obj, (HoloMap, DynamicMap)): 313 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:274, in layout_display(layout, max_frames) 271 max_frame_warning(max_frames) 272 return None --> 274 return render(layout) 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:494, in HoloViews._get_model(self, doc, root, parent, comm) 492 plot = self.object 493 else: --> 494 plot = self._render(doc, comm, root) 496 plot.pane = self 497 backend = plot.renderer.backend File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/panel/pane/holoviews.py:588, in HoloViews._render(self, doc, comm, root) 585 if comm: 586 kwargs['comm'] = comm --> 588 return renderer.get_plot(self.object, **kwargs) File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/renderer.py:239, in Renderer.get_plot(self_or_cls, obj, doc, renderer, comm, **kwargs) 236 defaults = [kd.default for kd in plot.dimensions] 237 init_key = tuple(v if d is None else d for v, d in 238 zip(plot.keys[0], defaults, strict=None)) --> 239 plot.update(init_key) 240 else: 241 plot = obj File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/plot.py:958, in DimensionedPlot.update(self, key) 956 def update(self, key): 957 if len(self) == 1 and key in (0, self.keys[0]) and not self.drawn: --> 958 return self.initialize_plot() 959 item = self.__getitem__(key) 960 self.traverse(lambda x: setattr(x, '_updated', True)) File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/plotly/plot.py:51, in PlotlyPlot.initialize_plot(self, ranges, is_geo) 50 def initialize_plot(self, ranges=None, is_geo=False): ---> 51 return self.generate_plot(self.keys[-1], ranges, is_geo=is_geo) File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/plotly/plot.py:206, in LayoutPlot.generate_plot(self, key, ranges, is_geo) 204 subplot = self.subplots.get((r, c), None) 205 if subplot is not None: --> 206 subplots = subplot.generate_plot(key, ranges=ranges, is_geo=is_geo) 208 # Computes plotting offsets depending on 209 # number of adjoined plots 210 offset = sum(r >= ir for ir in insert_rows) File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/plotly/plot.py:276, in AdjointLayoutPlot.generate_plot(self, key, ranges, is_geo) 273 # If no view object or empty position, disable the axis 274 if subplot: 275 adjoined_plots.append( --> 276 subplot.generate_plot(key, ranges=ranges, is_geo=is_geo) 277 ) 278 if not adjoined_plots: adjoined_plots = [None] 279 return adjoined_plots File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/plotly/element.py:746, in OverlayPlot.generate_plot(self, key, ranges, element, is_geo) 743 # propagate plot options to subplots 744 subplot.param.update(**plot_opts) --> 746 fig = subplot.generate_plot(key, ranges, el, is_geo=is_geo) 747 if figure is None: 748 figure = fig File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/plotly/element.py:186, in ElementPlot.generate_plot(self, key, ranges, element, is_geo) 184 # Get data and options and merge them 185 data = self.get_data(element, ranges, style, is_geo=is_geo) --> 186 opts = self.graph_options(element, ranges, style, is_geo=is_geo) 188 components = { 189 'traces': [], 190 'images': [], 191 'annotations': [], 192 'shapes': [], 193 } 195 for i, d in enumerate(data): 196 # Initialize traces File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/plotly/chart.py:68, in ScatterPlot.graph_options(self, element, ranges, style, **kwargs) 67 def graph_options(self, element, ranges, style, **kwargs): ---> 68 opts = super().graph_options(element, ranges, style, **kwargs) 69 cdim = element.get_dimension(self.color_index) 70 if cdim: File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/plotly/element.py:256, in ElementPlot.graph_options(self, element, ranges, style, is_geo, **kwargs) 252 opts.update( 253 showlegend=self.show_legend, legendgroup=element.group+'_'+legend) # make legendgroup unique for single trace enable/disable 255 if self._style_key is not None: --> 256 styles = self._apply_transforms(element, ranges, style) 258 # If style starts with '{_style_key}_', remove the prefix. This way 259 # a line_color property with self._style_key of 'line' doesn't end up 260 # as `line_line_color` 261 key_prefix_re = re.compile('^' + self._style_key + '_') File ~/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/plotly/element.py:381, in ElementPlot._apply_transforms(self, element, ranges, style) 379 if k in self._nonvectorized_styles: 380 element = type(element).__name__ --> 381 raise ValueError(f'Mapping a dimension to the "{k}" ' 382 'style option is not supported by the ' 383 f'{element} element using the {self.renderer.backend} ' 384 f'backend. To map the "{v.dimension}" dimension ' 385 f'to the {k} use a groupby operation ' 386 'to overlay your data along the dimension.') 388 # If color is not valid colorspec add colormapper 389 numeric = isinstance(val, np.ndarray) and dtype_kind(val) in 'uifMm' ValueError: Mapping a dimension to the "alpha" style option is not supported by the Points element using the plotly backend. To map the "dot" dimension to the alpha use a groupby operation to overlay your data along the dimension.
:Layout .Overlay.I :Overlay .Labels.I :Labels [rank,score] (text,align) .Points.I :Points [rank,score] (text,dot) .Overlay.II :Overlay .Labels.I :Labels [rank,score] (text,align) .Points.I :Points [rank,score] (text,dot)