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Comments (4)

HelenaLC avatar HelenaLC commented on July 18, 2024

Could you perhaps post imgData(spe) here as a code chunk? The above output of str() is hard to digest. Note that spatial_data is expected to be a SpatialExperiment for this to work.

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duyson1999 avatar duyson1999 commented on July 18, 2024

Hi, this is the class and content of imgData

class(spatial_data)
'SpatialExperiment'

imgData(spatial_data)
DataFrame with 1 row and 4 columns
sample_id image_id data scaleFactor
<character> <character> <list> <numeric>
1 10X_Mouse_Kidney hires #### 0.176991

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HelenaLC avatar HelenaLC commented on July 18, 2024

Hm, I can't see intuitively what's going wrong. Could you try

  1. Test that the plotting the image works, in principle:
library(SpatialExperiment)
plot(imgRaster(spatial_data))
  1. Use SPOTlight's internal function that is used to extract the image (this is being called by plotSpatialScatterpie), which is passed to plotImage where the error occurs.
x <- SPOTlight:::. extract_image(spatial_data)
class(x)
dim(x)

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