Staffli-class: The Staffli Class

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

The Staffli Class

Description

The Staffli object is a representation of images for Spatial Transcriptomics experiments that contains lists of scaled images in raster format and coordinates for the corresponding spots that can be used to map expression data onto the images.

Slots

imgs

A character vector of paths to the raw HE images.

rasterlists

A list of lists containing images in 'raster' format

scatter.data

Data.frame holding x, y, z coordinates for 3D interpolation and visualization

transformations

A list of 3x3 transformation matrices used to transform (x,y)-coordinates of an aligned image to a reference image.

meta.data

Contains meta-information about each spot, starting with regular (x,y)-coordinates found in the headers of gene-count matrices obtained with the ST method. The meta.data can also contain (adj_x, adj_y)-coordinates which are defined in the same grid but adjusted using the ST spot detector and (pixel_x, pixel_y)-coordinates which are defined in the coordinate system of the original image. Finally, a "sample" column is used to group the spots by image (capture area).

xdim

The width of the scaled images in pixels.

limits

Specifies the limits of the array (e.g. limits = c(100, 100) means that the array is a 100 spots wide and a 100 spots high)

dims

List of numerical vectors specifying the dimensions of the original images.

platforms

Specify the platform used to generate the ST data [options: 'Visium', '2k', '1k']

samplenames

Character specifying the samplenames.

pixels.per.um

Numeric vector specifying the number of pixels per micron

version

Package version.

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