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ococrook / hdxstats

hdxstats: An R-package for statistical analysis of hydrogen deuterium exchange mass-spectrometry data.
Apache License 2.0
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3D structure viewer #9

Closed ococrook closed 1 year ago

ococrook commented 2 years ago

Incoperate a 3D structure viewer, see here:

https://community.rstudio.com/t/three-dimensional-3d-interactive-visualization-of-protein-structures-shiny-contest-submission/104697

broncio123 commented 2 years ago

Testing API currently. Background colour parameter not working. Reported issue on repo https://github.com/nvelden/NGLVieweR/issues/5

ococrook commented 2 years ago

I just tried and it works for me

nvelden commented 2 years ago

Testing API currently. Background colour parameter not working. Reported issue on repo nvelden/NGLVieweR#5

This is an issue with the Rstudio Viewer. If you open the viewer in a browser you will see that it works.

broncio123 commented 2 years ago

Update Added proof of concept to map a list of random values associated with every residue and colour these according to some colour scale. The mapping works as: Residue -> Observable Value (e.g., Deu exposure)-> Colour image

broncio123 commented 1 year ago

This feature has already been implemented via visualise_hdx_data, as part of hdxstat-streamline.R, here https://github.com/ococrook/hdxstats/blob/77ab9c21681c9bce3c1721e9a9a5f3852dabd80a/R/hdxstat-streamline.R#L87

Note: This feature relies on the pdb-visualisation.R module, here https://github.com/ococrook/hdxstats/blob/app_v2/R/pdb-visualisation.R

An example of use can be found in https://github.com/ococrook/hdxstats/blob/app_v2/vignettes/tutorial-streamline.Rmd

I'll close this issue.