scanpy.pl.scatter#
- scanpy.pl.scatter(adata, x=None, y=None, color=None, use_raw=None, layers=None, sort_order=True, alpha=None, basis=None, groups=None, components=None, projection='2d', legend_loc='right margin', legend_fontsize=None, legend_fontweight=None, legend_fontoutline=None, color_map=None, palette=None, frameon=None, right_margin=None, left_margin=None, size=None, marker='.', title=None, show=None, save=None, ax=None)[source]#
Scatter plot along observations or variables axes.
Color the plot using annotations of observations (
.obs
), variables (.var
) or expression of genes (.var_names
).- Parameters:
- adata
AnnData
Annotated data matrix.
- x
Optional
[str
] (default:None
) x coordinate.
- y
Optional
[str
] (default:None
) y coordinate.
- color
str
|Collection
[str
] (default:None
) Keys for annotations of observations/cells or variables/genes, or a hex color specification, e.g., ‘ann1’, ‘#fe57a1’, or [‘ann1’, ‘ann2’].
- use_raw
Optional
[bool
] (default:None
) Whether to use raw attribute of adata. Defaults to True if .raw is present.
- layers
str
|Collection
[str
] (default:None
) Use the layers attribute of adata if present: specify the layer for x, y and color. If layers is a string, then it is expanded to (layers, layers, layers).
- basis
Optional
[Literal
['pca'
,'tsne'
,'umap'
,'diffmap'
,'draw_graph_fr'
]] (default:None
) String that denotes a plotting tool that computed coordinates.
- sort_order
bool
(default:True
) For continuous annotations used as color parameter, plot data points with higher values on top of others.
- groups
str
|Iterable
[str
] (default:None
) Restrict to a few categories in categorical observation annotation. The default is not to restrict to any groups.
- dimensions
0-indexed dimensions of the embedding to plot as integers. E.g. [(0, 1), (1, 2)]. Unlike components, this argument is used in the same way as colors, e.g. is used to specify a single plot at a time. Will eventually replace the components argument.
- components
str
|Collection
[str
] (default:None
) For instance, [‘1,2’, ‘2,3’]. To plot all available components use components=’all’.
- projection
Literal
['2d'
,'3d'
] (default:'2d'
) Projection of plot (default: ‘2d’).
- legend_loc
str
(default:'right margin'
) Location of legend, either ‘on data’, ‘right margin’ or a valid keyword for the loc parameter of
Legend
.- legend_fontsize
Union
[int
,float
,Literal
['xx-small'
,'x-small'
,'small'
,'medium'
,'large'
,'x-large'
,'xx-large'
],None
] (default:None
) Numeric size in pt or string describing the size. See
set_fontsize()
.- legend_fontweight
Union
[int
,Literal
['light'
,'normal'
,'medium'
,'semibold'
,'bold'
,'heavy'
,'black'
],None
] (default:None
) Legend font weight. A numeric value in range 0-1000 or a string. Defaults to ‘bold’ if legend_loc == ‘on data’, otherwise to ‘normal’. See
set_fontweight()
.- legend_fontoutline
float
(default:None
) Line width of the legend font outline in pt. Draws a white outline using the path effect
withStroke
.- colorbar_loc
Where to place the colorbar for continous variables. If None, no colorbar is added.
- size
UnionType
[int
,float
,None
] (default:None
) Point size. If None, is automatically computed as 120000 / n_cells. Can be a sequence containing the size for each cell. The order should be the same as in adata.obs.
- color_map
str
|Colormap
(default:None
) Color map to use for continous variables. Can be a name or a
Colormap
instance (e.g. “magma”, “viridis” or mpl.cm.cividis), seeget_cmap()
. If None, the value of mpl.rcParams[“image.cmap”] is used. The default color_map can be set usingset_figure_params()
.- palette
Union
[Cycler
,ListedColormap
,str
,tuple
[float
,...
],Sequence
[Union
[str
,tuple
[float
,...
]]]] (default:None
) Colors to use for plotting categorical annotation groups. The palette can be a valid
ListedColormap
name (‘Set2’, ‘tab20’, …), aCycler
object, a dict mapping categories to colors, or a sequence of colors. Colors must be valid to matplotlib. (seeis_color_like()
). If None, mpl.rcParams[“axes.prop_cycle”] is used unless the categorical variable already has colors stored in adata.uns[“{var}_colors”]. If provided, values of adata.uns[“{var}_colors”] will be set.- na_color
Color to use for null or masked values. Can be anything matplotlib accepts as a color. Used for all points if color=None.
- na_in_legend
If there are missing values, whether they get an entry in the legend. Currently only implemented for categorical legends.
- frameon
Optional
[bool
] (default:None
) Draw a frame around the scatter plot. Defaults to value set in
set_figure_params()
, defaults to True.- title
Optional
[str
] (default:None
) Provide title for panels either as string or list of strings, e.g. [‘title1’, ‘title2’, …].
- show
Optional
[bool
] (default:None
) Show the plot, do not return axis.
- save
UnionType
[str
,bool
,None
] (default:None
) If True or a str, save the figure. A string is appended to the default filename. Infer the filetype if ending on {‘.pdf’, ‘.png’, ‘.svg’}.
- ax
Optional
[Axes
] (default:None
) A matplotlib axes object. Only works if plotting a single component.
- adata
- Returns:
If show==False a
Axes
or a list of it.