CreateGiottoVisiumObject expr_data file about giotto HOT 6 CLOSED

Hi,

createGiottoVisiumObject expects you to give the path to the visium folder, which should have the following structure:

visium_folder:
- filtered_feature_bc_matrix
- raw_feature_bc_matrix
- spatial

Depending on whether you want to start from the raw or already pre-filtered data you can then either select 'raw' or 'filter' for the expr_data parameter.

Currently, we don't support reading directly from the .h5 file. I'll take a look and see how easy it would be to add this feature.

R

from giotto.

I've looked into it and I have updated the createGiottoVisiumObject. It can now also accept .h5 files directly. This should make it easier to create a Giotto object from Visium data. You'll need to reinstall Giotto (needs v1.0.3).

input paths

h5_file ='/your/path/Data/Visium_data/Breast_cancer_A/V1_Breast_Cancer_Block_A_Section_1_filtered_feature_bc_matrix.h5'
loc_file ='/your/path/Data/Visium_data/Breast_cancer_A/spatial/tissue_positions_list.csv'
png_file ='/your/path/Data/Visium_data/Breast_cancer_A/spatial/tissue_lowres_image.png'

command

giotto_visium = createGiottoVisiumObject(h5_visium_path = h5_file, 
 h5_tissue_positions_path = loc_file, 
 h5_image_png_path = png_file)

Please let me know if it works or if you encounter any problems. Thanks

from giotto.

I made a typo yesterday, which led to an error, but that's fixed now.

from giotto.

Hello,

Thank you so much for fixing this and I apologize for not getting back to this sooner to test it. I tried re-installing Giotto v1.0.3 using remotes::install_github("RubD/[email protected]") but I get a download error:

Downloading GitHub repo RubD/[email protected]
Error in utils::download.file(url, path, method = method, quiet = quiet, :
cannot open URL 'https://api.github.com/repos/RubD/Giotto/tarball/v1.0.3'

Is there another way?

from giotto.

Sorry, that was my fault. The current master version already had this feature, so you can just follow the normal installation instructions. I forgot to actually 'release' v1.0.3. I did that now, so also your previous command should work, but v1.0.3 is the same as the current version.

from giotto.

Thank you so much! The createGiottoVisiumObject wasn't able to read the h5 file earlier despite re-installing, so I figured I needed to explicitly install v1.0.3. However, it's all fixed now, thanks so much for the prompt help always. Looking forward to test all the new functionalities that have been added since I last ran the spatial vignette.

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