New intro guide #123
New intro guide #123
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View / edit / reply to this conversation on ReviewNB ckmah commented on 2024-11-14T15:23:15Z rename |
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View / edit / reply to this conversation on ReviewNB ckmah commented on 2024-11-14T15:23:16Z show how to convert to pandas with compute(), also fix markdown ^ |
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View / edit / reply to this conversation on ReviewNB ckmah commented on 2024-11-14T15:23:17Z add note about not doing color if too many categories melonora commented on 2024-11-27T10:13:35Z what do you mean with this comment? ckmah commented on 2024-11-29T07:51:46Z ah i meant to add a note that recommends against plotting with too many categories or else rendering the legend is very slow (matplotlib). not super necessary |
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View / edit / reply to this conversation on ReviewNB ckmah commented on 2024-11-14T15:23:17Z add can use geopandas (and link) for geometric operations |
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View / edit / reply to this conversation on ReviewNB ckmah commented on 2024-11-14T15:23:18Z explain what this is plotting (gene expression) |
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View / edit / reply to this conversation on ReviewNB ckmah commented on 2024-11-14T15:23:19Z and cell type |
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View / edit / reply to this conversation on ReviewNB ckmah commented on 2024-11-14T15:23:20Z format sdata\ .pl.render(...)\ .plshow() |
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View / edit / reply to this conversation on ReviewNB ckmah commented on 2024-11-14T15:23:21Z if have time, better more interesting polygon? |
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View / edit / reply to this conversation on ReviewNB ckmah commented on 2024-11-14T15:23:22Z remove data directory |
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View / edit / reply to this conversation on ReviewNB ckmah commented on 2024-11-14T15:23:23Z fix markdown |
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what do you mean with this comment? View entire conversation on ReviewNB |
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View / edit / reply to this conversation on ReviewNB melonora commented on 2024-11-27T10:18:01Z Maybe for tables we could add a link to the notebook explaining them. Also, in the codebase elements are also refered to as either |
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View / edit / reply to this conversation on ReviewNB melonora commented on 2024-11-27T10:18:01Z for supported platforms -> for supported spatial omics platforms... perhaps doc link here |
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View / edit / reply to this conversation on ReviewNB melonora commented on 2024-11-27T10:18:02Z One could interpret 2D here as XY and 3D as CYX. Perhaps put it like this:
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View / edit / reply to this conversation on ReviewNB melonora commented on 2024-11-27T10:18:03Z This method is being deprecated due to the definition being ambigious, am I getting the actual channels or the channel names. A method |
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The plotting warnings regarding |
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Also regarding terms, might be nice to later link to the glossary, but that would be a separate issue. |
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ah i meant to add a note that recommends against plotting with too many categories or else rendering the legend is very slow (matplotlib). not super necessary View entire conversation on ReviewNB |
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@melonora thanks for the review, addressed comments by compiling tutorial links in first text block as suggested. also added the notebook to the Tutorials table of contents |
Create a new intro guide; the goal is to lower the barrier to entry and highlight core SpatialData framework functionality and plotting via
spatialdata-plot.Related main issue: scverse/spatialdata#748