addRoiScatter

addRoiScatter

addRoiScatter(
    data,
    method=None,
    marker=None,
    threshold=0.5,
    raw=False,
    log=False,
    subset=None,
    imageId="imageid",
    xCoordinate="X_centroid",
    yCoordinate="Y_centroid",
    size=5,
    cmap="gist_heat",
    lassoAlpha=0.8,
    lassoLinewidth=3,
    lassoColor="red",
    roiName="selected_roi",
    label="roi_scatter",
    sdataTable=None,
)

Label a region of interest by thresholding a marker.

scimap's addROI_scatter opened a Matplotlib window and let you lasso cells by hand. That does not work in a script, a notebook running headless, or CI, so the scimappro version defines the ROI by a rule instead: cells above threshold for marker are labelled roiName, everything else 'Other', and the result goes into obs[label].

It is a thin wrapper over sp.tl.classify; use that directly when you want more than one positive marker or a negative one.

For hand-drawn ROIs, draw them in OMERO and import them with sp.helpers.addROI_omero.

Parameters:

Name	Type	Description	Default
data	(AnnData | SpatialData | str, required)	The cell table. An AnnData, a path to an .h5ad file, a SpatialData object, or a path to a .zarr SpatialData store.	required
method	str	Accepted for signature compatibility with scimap. Only marker thresholding is implemented.	None
marker	(str | list, required)	The marker(s) whose intensity defines the ROI. A ValueError is raised when omitted.	None
threshold	float	Cells at or above this value are inside the ROI. 0.5 is the boundary on data rescaled by sp.pp.rescale.	0.5
raw	bool	Accepted for signature compatibility with scimap.	False
log	bool	Accepted for signature compatibility with scimap.	False
subset	str | list	Accepted for signature compatibility with scimap.	None
imageId	str	Column in obs holding image identifiers.	'imageid'
xCoordinate	str	Column in obs holding x positions.	'X_centroid'
yCoordinate	str	Column in obs holding y positions.	'Y_centroid'
size	float	Accepted for signature compatibility with scimap's interactive plot.	5
cmap	str	Accepted for signature compatibility with scimap's interactive plot.	'gist_heat'
lassoAlpha	float	Accepted for signature compatibility with scimap's interactive plot.	0.8
lassoLinewidth	float	Accepted for signature compatibility with scimap's interactive plot.	3
lassoColor	str	Accepted for signature compatibility with scimap's interactive plot.	'red'
roiName	str	Label given to cells inside the ROI.	'selected_roi'
label	str	Column in obs the ROI labels are written to.	'roi_scatter'
sdataTable	str	Which SpatialData table to use.	None

Returns:

Name	Type	Description
adata	AnnData | SpatialData	The input with obs[label] set to roiName or 'Other'.

Example

adata = sp.pl.addRoiScatter(
    adata, marker="ECAD", threshold=0.5, roiName="tumour", label="roi"
)
adata.obs["roi"].value_counts()

sp.pl.spatialScatterPlot(adata, colorBy="roi", s=3)