pegasus.spatial¶
- pegasus.spatial(data, attrs=None, basis='spatial', resolution='hires', cmaps='viridis', vmin=None, vmax=None, alpha=1.0, alpha_img=1.0, dpi=300.0, return_fig=False, **kwargs)[source]¶
Scatter plot on spatial coordinates. This function is inspired by SCANPY’s pl.spatial function.
- Parameters
data (
pegasusio.MultimodalData
orpegasusio.UnimodalData
oranndata.AnnData
) – Use current selected modality in data.attr (
str
, optional, default:None
) – Color scatter plots by attribute ‘attr’. This attribute should be one key in data.obs, data.var_names (e.g. one gene) or data.obsm (attribute has the format of ‘obsm_key@component’, like ‘X_pca@0’). If it is categorical, a palette will be used to color each category separately. Otherwise, a color map will be used. IfNone
, just plot data points of the same color.basis (
str
, optional, default:spatial
) – Basis to be used to generate spatial plots. Must be the 2D array showing the spatial coordinates of data points.resolution (
str
, optional, default:hires
) – Use the spatial image whose value is specified indata.img['image_id']
to show in background. For 10X Visium data, user can either specifyhires
orlowres
to use High or Low resolution spatial images, respectively.cmaps (
str
orList[str]
, optional, default:viridis
) – The colormap(s) for plotting numeric attributes. The defaultviridis
colormap theme follows the spatial plot function in SCANPY (scanpy.pl.spatial
).vmin (
float
, optional, default:None
) – Minimum value to show on a numeric scatter plot (feature plot).vmax (
float
, optional, default:None
) – Maximum value to show on a numeric scatter plot (feature plot).alpha (
float
orList[float]
, optional, default:1.0
) – Alpha value for blending the attribute layers, from 0.0 (transparent) to 1.0 (opaque). If this is a list, the length must match attrs, which means we set a separate alpha value for each attribute.alpha_img (
float
, optional, default:1.0
) – Alpha value for blending the background spatial image, from 0.0 (transparent) to 1.0 (opaque).dpi (
float
, optional, default:300.0
) – The resolution of the figure in dots-per-inch.return_fig (
bool
, optional, default:False
) – Return aFigure
object ifTrue
; returnNone
otherwise.
- Returns
A
matplotlib.figure.Figure
object containing the dot plot ifreturn_fig == True
- Return type
Figure
object
Examples
>>> pg.spatial(data, attrs=['louvain_labels', 'Channel']) >>> pg.spatial(data, attrs=['CD14', 'TRAC'], resolution='lowres')