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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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Error in generating visium object in Giotto in R studio : Object 'visium_png' not found #807

Closed hndyilm closed 10 months ago

hndyilm commented 10 months ago

Hello everyone,

While generating visium object in Giotto in R studio, I get an error:

instrs = createGiottoInstructions( python_path = 'C:/Users/AppData/Local/r-miniconda/envs/giotto_env/python.exe', save_plot = TRUE, show_plot = FALSE)

data_path = 'C:/Users/Desktop/outs/'

visium_SARC = createGiottoVisiumObject(visium_dir = data_path, expr_data = 'raw', h5_tissue_positions_path = 'C:/Users/Desktop/outs/spatial/tissue_positions.csv', h5_image_png_path = 'C:/Users/Desktop/outs/spatial/', png_name = 'tissue_hires_image.png', do_manual_adj = FALSE, gene_column_index = 2, instructions = instrs)

ERROR: Error in createGiottoVisiumObject(visium_dir = data_path, expr_data = "raw", : Object 'visium_png' not found

Any help would be appreciated. Thanks.

RubD commented 10 months ago

Can you share which version of Giotto you're using? I'd suggest to use the latest version and carefully read the help page for the createGiottoVisiumObject. You can start from a Visium directory or a .h5 file, but your parameters seem to suggest a combination of both.

We realize that this is a bit confusing and we will likely separate the .h5 and directory workflows in the future.

hndyilm commented 10 months ago

I am using the last version of Giotto (3.3.0). Thanks.