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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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File does not exit #1007

Closed 13954380607 closed 2 months ago

13954380607 commented 2 months ago

Provide path to your data folder

data_path = '/home/dl2373/new/raw_feature_bc_matrix/'

Create Giotto Visium Object

visium_kidney = createGiottoVisiumObject(visium_dir = data_path,

  • expr_data = 'raw',
  • png_name = 'tissue_lowres_image.png',
  • gene_column_index = 2,
  • instructions = instrs) A structured visium directory will be used Error: [Giotto] /home/dl2373/new/raw_feature_bc_matrix/ does not exist! Description: I have a raw data in this direction, but I don't understand why it always gave me that this file doesn't exit. Is it because the Giotto package is wrong? Thank you
RubD commented 2 months ago

Try with: data_path = '/home/dl2373/new/'

And also check dir.exists(data_path)

13954380607 commented 2 months ago

Thank you so much!

jiajic commented 2 months ago

Guessing this is resolved. Please reopen if not.