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fix: VisiumV1 definition location #165

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wants to merge 22 commits into from
Closed

fix: VisiumV1 definition location #165

wants to merge 22 commits into from

Commits on Feb 2, 2024

  1. Added spatial_network and nn_network in seuratToGiotto functions plus… 

    … updated image in giottoToSeurat
    @iqraAmin
    iqraAmin committed Feb 2, 2024
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Commits on Feb 4, 2024

  1. Merge pull request drieslab#162 from iqraAmin/dev 

    Added spatial_network and nn_network in seuratToGiotto functions plus…
    @jiajic
    jiajic authored Feb 4, 2024
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Commits on Feb 6, 2024

  1. new: createNetwork() generic 

    - make generic function `createNetwork()`
- new method for all matrices to create sNN and kNN networks. Flexibly allows inclusion of weight, distance cols and name attributes. Allows return as data.table or igraph
    @jiajic
    jiajic committed Feb 6, 2024
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Commits on Feb 11, 2024

  1. feat: WIP createNetwork() hub function 

    Still needs further work aligning all the params and making obvious things to edit in order to get similar behavior to default Giotto operations
    @jiajic
    jiajic committed Feb 11, 2024
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Commits on Feb 13, 2024

  1. chore: remove stray browser()

    @jiajic
    jiajic committed Feb 13, 2024
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  2. chore: use setDT instead of as.data.table

    @jiajic
    jiajic committed Feb 13, 2024
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  3. chore: improve docs and comments for convert_to_full_spatial_network()

    @jiajic
    jiajic committed Feb 13, 2024
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  4. chore: improve docs for convert_to_full_spatial_network()

    @jiajic
    jiajic committed Feb 13, 2024
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  5. feat: add compatibility for spatial network DTs that do not have coor… 

    …ds info in `convert_to_reduced_spatial_network()`
    @jiajic
    jiajic committed Feb 13, 2024
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  6. chore: document convert_to_reduced_spatial_network()

    @jiajic
    jiajic committed Feb 13, 2024
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  7. feat: edge distance calculation edge_distances() 

    Add function to calculate euclidean distances for any m x n matrix when provided a data.table of `from` and `to` interactions
    @jiajic
    jiajic committed Feb 13, 2024
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  8. feat: createNetwork() 

    Refactors Giotto's spatial and NN networks creation into a hub function that allows starting directly from matrix data.

Added tests that currently only ensure parity with original implementation.
    @jiajic
    jiajic committed Feb 13, 2024
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  9. chore: fix merge conflict

    @jiajic
    jiajic committed Feb 13, 2024
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  10. chore: run document

    @jiajic
    jiajic committed Feb 13, 2024
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  11. chore: change createNetwork() to non-generic function 

    Avoids needing to import matrix class definitions.
    @jiajic
    jiajic committed Feb 13, 2024
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Commits on Feb 14, 2024

  1. chore: fix network test script

    @jiajic
    jiajic committed Feb 14, 2024
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  2. chore: change deprecated igraph function names

    @jiajic
    jiajic committed Feb 14, 2024
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  3. chore: fixes for rcmdcheck

    @jiajic
    jiajic committed Feb 14, 2024
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  4. fix: alternative method of creating VisiumV1 

    Try to avoid import of SeuratObject
    @jiajic
    jiajic committed Feb 14, 2024
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  5. chore: fix edge_distances() example

    @jiajic
    jiajic committed Feb 14, 2024
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  6. Merge branch 'dev' into VisiumV1_tryfix

    @jiajic
    jiajic committed Feb 14, 2024
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  7. fix: VisiumV1 definition

    @jiajic
    jiajic committed Feb 14, 2024
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