The goal of shinySTRegister is to provide a simple (if barebones) interface for registering (i.e. aligning) two spatial transcriptomics samples. This is done by specifying three points on the first sample (to be aligned) and their corresponding projections on the second (reference) sample.
The corresponding affine transformation is then determined and applied to the first sample, which can be saved as RDS for future use.
You can install the development version of shinySTRegister from GitHub with:
# install.packages("devtools")
devtools::install_github("JonSulc/shinySTRegister")
Given two samples (to_align and reference) loaded as SpatialExperiment objects, the interface can be started with:
library(shinySTRegister)
shiny_register(to_align, reference, nbins = 400)
The nbins
parameter controls the resolution of the image, counts being binned
into a grid of
To help with the setup for this, there are a few convenience functions for the
loading and display of data from certain technologies.
load_as_spatial_experiment
takes a counts filename (spot/cell SpatialExperiment
object. The id_columns
argument specifies the columns
identifying the corresponding spots or cells to combine the data. If NULL
,
they are assumed to be in the