S4 giottoImage Class

Framework of giotto object to store and work with spatial expression data

Value

giottoImage

Details

[mg_object] Core object is any image that can be read by the magick package

[boundaries] Boundary adjustments can be used to manually or automatically through a script adjust the image with the spatial data.

Slots

name

name of Giotto image

mg_object

magick image object

minmax

minimum and maximum of associated spatial location coordinates

boundaries

x and y coordinate adjustments (default to 0)

scale_factor

image scaling relative to spatial locations

resolution

spatial location units covered per pixel

file_path

file path to the image if given

OS_platform

Operating System to run Giotto analysis on

Examples

giottoImage()
#> An object of class ' giottoImage ' with name  test 
#>  
#> Min and max values are: 
#>  Max on x-axis:  
#>  Min on x-axis:  
#>  Max on y-axis:  
#>  Min on y-axis:  
#>  
#> Boundary adjustment are: 
#>  Max adjustment on x-axis:  
#>  Min adjustment on x-axis:  
#>  Max adjustment on y-axis:  
#>  Min adjustment on y-axis:  
#>  
#> Boundaries are: 
#>  Image x-axis max boundary:   
#>  Image x-axis min boundary:   
#>  Image y-axis max boundary:   
#>  Image y-axis min boundary:   
#>  
#> Scale factor: 
#> NULL
#> 
#>  Resolution: 
#> NULL
#> 
#>  File Path: 
#> NULL