prep_stitched_data: Prepare stitched data for plotting

In LieberInstitute/spatialLIBD: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Prepare stitched data for plotting

Description

Given a SpatialExperiment built with visiumStitched::build_spe() http://research.libd.org/visiumStitched/reference/build_spe.html, drop excluded spots (specified by spe$exclude_overlapping) and compute an appropriate spot size for plotting with vis_gene() or vis_clus(), assuming the plot will be written to a PDF of default dimensions (i.e. width = 7 and height = 7).

Usage

prep_stitched_data(spe, point_size, image_id)

Arguments

spe	A SpatialExperiment built with visiumStitched::build_spe(), containing a logical spe$exclude_overlapping column specifying which spots to display in plots
point_size	A numeric(1) specifying the size of the points. Defaults to 1.25. Some colors look better if you use 2 for instance.
image_id	A character(1) with the name of the image ID you want to use in the background.

Value

A list with names spe and point_size containing a filtered, ready-to-plot SpatialExperiment and an appropriate spot size (passed to vis_gene() or vis_clus()), respectively

Author(s)

Nicholas J. Eagles

LieberInstitute/spatialLIBD documentation built on July 17, 2024, 5:05 a.m.