GetCropWindows: Get crop geometries

In jbergenstrahle/STUtility: Analysis and visualization of Spatial Transcriptomics data

Get crop geometries

Description

This function can be used to define "crop windows" based on sets of target spots.

Usage

GetCropWindows(
  object,
  group.by = NULL,
  groups.to.keep = NULL,
  symmetric = TRUE,
  keep.all.spots = FALSE,
  xy_padding = 50
)

Arguments

object	A Seurat object created with STutility
group.by	A meta.data column to group the spots by. Only character vector or factors are allowed. Selects "labels" by default.
groups.to.keep	Provide a caharcter vector of groups to keep.
symmetric	Make crop window square. This will mkae it easier to align images in dowstream processing steps.
keep.all.spots	Keep all spots within selected crop windows and not just the spots belonging to the predefined groups. All spots that are present in multiple crop windows will be removed.
xy_padding	Increase the crop area in all directions. Given in pixels.

Value

A list of "crop geometries" to be used with CropImages)

jbergenstrahle/STUtility documentation built on March 14, 2023, 7:15 a.m.