A question about spatPlot() function

[jhyhy0825]

I used spatPlot() function and I got the result turned 90 degrees to the left. I extracted counts matrix and location matrix from Seurat object. I attached my code below. Let me know if there's a solution. Thank you.

count <- data@assays$Spatial@counts count <- data.matrix(count) location <- GetTissueCoordinates(data) location <- data.matrix(location) Giotto <- createGiottoObject(raw_exprs=count,spatial_locs=location) mg_img = magick::image_read(image) mypl = spatPlot(Giotto, return_plot = T, point_alpha = 0.8) orig_png = createGiottoImage(gobject = Giotto, mg_object = mg_img, name = 'image', xmax_adj = 450, xmin_adj = 550, ymax_adj = 200, ymin_adj = 200) mypl_image = addGiottoImageToSpatPlot(mypl, orig_png)

[mattobny]

Hello @jhyhy0825, would you be able to share your data so that I can try to reproduce this? Also, are you able to provide screenshots indicating the original, desired plot, and the rotated result? I am also gently assuming that the results from spatPlot() are rotated, while the image is not; please clarify this if I am assuming incorrectly.

[jiajic]

To add onto this, if it's only the spatial locations that are the issue, in Giotto Suite right now, there are internal functions for rotating spatial locations using radians

library(Giotto)
library(GiottoData)

# load test data
viz = loadGiottoMini('vizgen')

# get spatLocsObj
spatlocs = Giotto:::get_spatial_locations(viz)

# rotate spatial locations 90 deg clockwise (pi/2 radians)
# rotation center assumed to be the center of the x and y ranges
spatlocs[] = rotate_spatial_locations(
  spatlocs[],
  rotateradians = c(xy = pi/2, zy = 0, xz = 0),
  rcenter = c(x = mean(range(st[]$sdimx)), y = mean(range(st[]$sdimy)), z = 0)
)
viz = set_spatial_locations(viz, spatlocs = spatlocs)

Currently on our dev branch suite_dev, we also have the spin() generic that wraps the former code and works for spatLocsObj as well

plot(spatlocs)
spatlocs = spin(spatlocs, 90)
plot(spatlocs)