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jfnavarro / st_viewer

A GUI tool for easy and smooth visualisation and analysis of Spatial Transcriptomics datasets
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Problem running PCA/t-SNE #46

Open footie11 opened 3 years ago

footie11 commented 3 years ago

I am having issues getting any of the data analysis parts to work on Windows.

Do you have the specific requirements for R and its packages available.

Also, is there a way to turn on debugging, so I can see what is failing.

Thanks Simon

jfnavarro commented 3 years ago

Hi Simon,

Which version are you using? You should not need R unless you use an old version.

Best, Jose

footie11 commented 3 years ago

I am using the latest version 0.8.5.

footie11 commented 3 years ago

In the master branch, the AnalysisPCA.cpp file still references the RInterface and also seems to reference missing files in git. ex. AnalysisPCA.h is missing.

Could you post a new Windows release based on all the recent updates to see if that makes a difference.

Cheers Simon

jfnavarro commented 3 years ago

AnalysisPCA.cpp is not being used in the tool (take a look to the CMakeList.txt file). I kept it in the repository just in case I want to add that functionality again in the future.

The class that implements the clustering (PCA/t-SNE) is called AnalysisClustering.cpp

If a file was missing in the tool It would not compile. It is okay to have source code in a repository that is not included in the tool or used.

There is nowhere in the tool that makes uses of R so your issue has to be related to something else.

I plan to make a release soon. However, it would be nice to get more details on your issue.

Best, Jose

footie11 commented 3 years ago

Whenever I try to run one of the Analysis clustering options it returns with an error. (There was an error performing the unsupervised clustering) I don't have an issue viewing the spots on the tissue or viewing genes.

footie11 commented 3 years ago

In case it is an issue with our data, I was going to test with the test data but the spot coordinates file is missing in the Data directory.

jfnavarro commented 3 years ago

I can provide you the spot coordinates (I am planning to update the test data in the next release). Could you give me your email address?