Option to Zoom or Crop Images in SpaCET.visualize.spatialFeature

[Altsplicer]

Hi,
Thanks for developing this great package — I really appreciate your work! I was wondering if there’s a way to zoom in or crop images generated using the SpaCET.visualize.spatialFeature function. One of my tissue samples contains a lot of background space, and I’d like to focus the output on just the tissue region and the captured expression spots.

Is there currently a way to do this, or would it be possible to implement such a feature?

Thanks in advance!

[beibeiru]

Hi, @Altsplicer ,

Thank you for this great suggestion and the previous one (#20)!
I will let you know once I implement them soon.

Best,
Beibei

[beibeiru]

Hi, @Altsplicer,

Please reinstall our package. You can set imageSize = "CaptureArea" to show the capture area only.

library(SpaCET)
visiumPath <- file.path(system.file(package = "SpaCET"), "extdata/Visium_BC")
SpaCET_obj <- create.SpaCET.object.10X(visiumPath = visiumPath)
SpaCET_obj <- SpaCET.quality.control(SpaCET_obj, min.genes=100)

SpaCET.visualize.spatialFeature(
  SpaCET_obj, 
  spatialType = "QualityControl", 
  spatialFeatures=c("UMI"),
  imageBg = TRUE,
  imageSize = "CaptureArea"
)

If you want to crop the green region, you can set imageSize = "CustomizedArea" and also assign 4 numbers (0~1) to CustomizedAreaScale, corresponding to the figure above (x_left, x_right, y_bottom, y_top).

SpaCET.visualize.spatialFeature(
  SpaCET_obj, 
  spatialType = "QualityControl", 
  spatialFeatures=c("UMI"),
  imageBg = TRUE,
  imageSize = "CustomizedArea",
  CustomizedAreaScale = c(0, 0.2, 0, 0.3)
)