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CRI-iAtlas / iatlas-app

R Shiny app for CRI iAtlas, an interactive web portal for exploring immuno-oncology data. (iAtlas portal 2022 and beyond)
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Cellimage Illustration not loking correct #67

Closed andrewelamb closed 3 years ago

andrewelamb commented 3 years ago

The Cellimage illustration has some issues vs how it looks in v1.3

vthorsson commented 3 years ago

Things to look into: From load_data.R, do cellimage_base <- load_cellimage_base() (possibly need to extract cellimage_base down one layer in object returned). Inspect things like image_grob and pathlabels in that object and compare with 1.3.

Be aware that pathlabels[1:44] may have been edited to pathlabels[1:43] in functions/cellimage.utils.R to get the module to display an image.

vthorsson commented 3 years ago

A possible shift may have happened in updates of grid and grImport2 pages. grImport2 has however not been updated this year.

vthorsson commented 3 years ago

From @andrewelamb : The branch you'll want to look in is: https://github.com/CRI-iAtlas/iatlas-app/tree/mv_cellimage_module_to_api

vthorsson commented 3 years ago

Turned out main issue was the CD 8 T cell entry was missing from the file containing image objects labels. Has been corrected, on the above branch

andrewelamb commented 3 years ago

@vthorsson

https://isb-cgc.shinyapps.io/iatlas-v2-staging/ has these updates. It looks like the text resolution isn't as sharp as before. I'll leave it to you if you want to re-open this issue.