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shamansim / Vizection

Shiny application for single cell transcriptomics studies data visualisation / exploration and quality control
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Support for SummarizedExperiment objects. #12

Closed charles-plessy closed 6 years ago

charles-plessy commented 7 years ago

Bonjour Simon,

these "genes" and "libs" were just a clumsy attempt to reach what the authors of the SummarizedExperiment package did much better.

I think that it would be great for Vizection to at least support SummarizedExperiment objects natively, and perhaps even later drop support for genes/libs table (in favor of explaining how to make a SummarizedExperiment with them).

This pull request lets Vizection load a SummarizedExperiment, and then internally turn it into genes/libs tables. Had I more time, I would have liked to make deeper changes where Vizection's functions would use the SE object directly via the colData and assay functions...

What do you think about it ?

shamansim commented 6 years ago

Bonjour Charles,

I think for now, the points to focus on are the accessibility and documentation of the package. Connecting to the GenomicRange object is a good step. I really think that using S4 objects and their methods is a good way to increase reproducibility in the processing of the data. I agree with the idea of droping the 'not standard' genes/libs table.

How about using the dedicated methods for the manipulation of the SummerizedExperiment object inside Vizection ? It can be long work for now but a strength for later if there are new contributors.

Thanks