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Error while updating Giotto Image #1053

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unikill066 opened this issue Oct 17, 2024 · 0 comments
Open

Error while updating Giotto Image #1053

unikill066 opened this issue Oct 17, 2024 · 0 comments

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@unikill066
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Creating Giotto Image:

>   visium_data <- createGiottoVisiumObject(visium_dir = NULL,
+                                           h5_visium_path = file.path(file_path, "raw_feature_bc_matrix.h5"),
+                                           h5_tissue_positions_path = file.path(file_path, "spatial", "tissue_positions_list.csv"),
+                                           h5_image_png_path = file.path(file_path, "spatial", "tissue_lowres_image.png"),
+                                           h5_json_scalefactors_path = file.path(file_path, "spatial", "scalefactors_json.json"),
+                                           png_name = "tissue_lowres_image.png",
+                                           instructions = instrs)
A path to an .h5 10X file was provided and will be used
 - found image
 - found scalefactors. attempting automatic alignment for the 'lowres' image

Updating Giotto Image:

> visium_data <- updateGiottoImage(visium_data, image_name = 'image',
+                                    xmax_adj = xmax_adj, xmin_adj = xmin_adj,
+                                    ymax_adj = ymax_adj, ymin_adj = ymin_adj)
Error in get_giottoImage_MG(gobject = gobject, name = image_name) : 
  No giottoImages have been found 
> showGiottoImageNames(visium_data)
Image type: largeImage 

--> Name: image 

Error:

Error in get_giottoImage_MG(gobject = gobject, name = image_name) : 
  No giottoImages have been found 
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