SeuratCropper

Crops a Seurat Object using a sf polygon. Only cells and molecules inside the polygon are retained.
If no cells remain after the cropping the FOV is returned unchanged with a warning.

Description

Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.

Installation

Depends on:

• Seurat
• sf
• data.table

Recommended:

• geojsonsf

Usage

QPath:

1. Open the image corresponding to the FOV to crop in Seurat.
2. Draw the region to crop as a polygon annotation:
   https://qupath.readthedocs.io/en/0.3/docs/reference/commands.html#polygon
   The wand tool could also work:
   https://qupath.readthedocs.io/en/0.3/docs/reference/commands.html#wand-tool
3. Export the annotation as geojson file:
   https://qupath.readthedocs.io/en/0.3/docs/advanced/exporting_annotations.html#geojson

R Setup:

library(Seurat)
library(data.table)
library(sf)
library(geojsonsf)

Read in a polygon from a geojson file:

Polygon_A <- geojson_sf("cropping/B.geojson")
Polygon_B <- geojson_sf("cropping/A.geojson")

Subset the Seurat Objecet:

subsetted_object <- PolygonCropSeurat(object, list(FOV_A = Polygon_A, FOV_B = Polygon_B))

TODO

To do:

• Setup so cell polygons can be used instead of centroid.
• Fail with an Error if no centroids are available