zktuong/dandelion: v0.2.2
In: oai:zenodo.org:6759792; (2022)
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Elektronische Ressource
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What's Changed try and add youtube video to docs by @zktuong in https://github.com/zktuong/dandelion/pull/148 testing_rpy2_update by @zktuong in https://github.com/zktuong/dandelion/pull/150 Speed upgrade - Refactor generate network by @zktuong in https://github.com/zktuong/dandelion/pull/152 remove nxviz from requirements by @zktuong in https://github.com/zktuong/dandelion/pull/157 Bug fixes and Improvements Speed up generate_network pair-wise hamming distance is calculated on per clone/clonotype only if more than 1 cell is assigned to a clone/clonotype .distance slot is removed and is now directly stored/converted from the .graph slot. new options: compute_layout: bool = True. If dataset is too large, generate_layout can be switched to False in which case only the networkx graph is returned. The data can still be visualised later with scirpy's plotting method (see below). layout_method: Literal['sfdp', 'mod_fr'] = 'sfdp'. New default uses the ultra-fast C++ implemented sfdp_layout algorithm in graph-tools to generate final layout. sfdp stands for Scalable Force Directed Placement. Minor caveat is that the repulsion is not as good - when there's a lot of singleton nodes, they don't separate well unless you some how work out which of the parameters in sfdp_layout to tweak will produce an effective separate. changing gamma alone doesn't really seem to do much. The original layout can still be generated by specifying layout_method = 'mod_fr'. Requires a separate installation of graph-tool via conda (not managed by pip) as it has several C++ dependencies. pytest on macos may also stall because of a different backend being called - this is solved by changing tests that calls generate_network to run last. added steps to reduce memory hogging. min_size was doing the opposite previously and this is now fixed. #155 Speed up transfer Found a faster way to create the connectivity matrix. this also now transfer a dictionary that scirpy can use to generate the plots https://github.com/scverse/scirpy/issues/286 Fix #153 ...
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zktuong/dandelion: v0.2.2
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Autor/in / Beteiligte Person: | Zewen Kelvin Tuong ; Polanski, Krzysztof ; Sturm, Gregor |
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Quelle: | oai:zenodo.org:6759792; (2022) |
Veröffentlichung: | 2022 |
Medientyp: | Elektronische Ressource |
DOI: | 10.5281/zenodo.6759792 |
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