How to get an affine transformation matrix

[Bon-jour]

Dear VoltRon Development Team,
I am writing to express my sincere gratitude for developing VoltRon. It has been an invaluable tool for our spatial transcriptomics research and has greatly facilitated our work.
However, I have encountered a question while using the package. After performing spatial registration using registerSpatialData(), I am unsure how to extract the specific coordinate correspondence (mapping relationship) between the two different spatial datasets (e.g., Xenium and Visium).
Could you please advise on how to retrieve the aligned coordinates or the mapping table that links the spots/cells between the two assays?
Thank you very much for your time and assistance.
Best regards

[Artur-man]

Dear @Bon-jour,

Thanks so much for your kind words! I am glad that our package is this useful in your research.

Absolutely, let me walk you though how to get the mapping:

library(VoltRon)

Xen_R1 <- importXenium("data/VisiumXenium/10X_Xenium_Visium/Xenium_R1/outs/", sample_name = "XeniumR1",
                       resolution_level = 7, overwrite_resolution = TRUE, import_molecules = FALSE)
Xen_R2 <- importXenium("data/VisiumXenium/10X_Xenium_Visium/Xenium_R2/outs/", sample_name = "XeniumR2",
                       resolution_level = 7, overwrite_resolution = TRUE, import_molecules = FALSE)
Vis <- importVisium("data/VisiumXenium/10X_Xenium_Visium/Visium/", sample_name = "VisiumR1")

Xen_R2 <- modulateImage(Xen_R2, brightness = 400)
xen_reg <- registerSpatialData(object_list = list(Xen_R1, Vis, Xen_R2))

Now if you go to the mapping component of mapping_parameters. Since there are three datasets here there are no mapping parameters of the second data (in the middle), first mapping is the transformation matrix that warps from data1 to data2 ... the third is the matrix from data3 to data2. Thus all coordinates are mapped to data2 coordinates.

In case of two datasets, mapping will be from data2 to data1.

> xen_reg$mapping_parameters$mapping
$`1`
$`1`[[1]]
$`1`[[1]][[1]]
            [,1]       [,2]      [,3]
[1,]  0.68573175 0.03686681  97.68145
[2,] -0.03798783 0.69005239 182.51073

$`1`[[1]][[2]]
NULL



$`2`
NULL

$`3`
$`3`[[1]]
$`3`[[1]][[1]]
            [,1]        [,2]      [,3]
[1,]  0.68772330 0.008755365 115.64245
[2,] -0.01630314 0.694710917  78.32366

$`3`[[1]][[2]]
NULL