Test/Review OsteoBioR updates for plots

[arunge]

@isomemo Except of one left point all other features are implemented with version 24.04.1 and ready for testing on the beta version. Feel free to test the updates

• [x] Option to choose plot(s) symbols and colours -> https://github.com/Pandora-IsoMemo/osteo-bior/pull/44 (1)
• [x] Option to add/edit plot(s) legend (2)
• [x] When having two y-axes (one on the left and another one on the right of the plot). Have the option to switch their positions. (3)
• In the export of plot results include columns for: (4)
  • [x] median value of interval and
  • [x] corresponding y value (and
  • [x] SD and
  • [x] user set credible interval).
  • [ ] Users can use default options or select a temporal resolution (x-axis) for sampling of y values.
  • [x] A column gives row number (1,2,3…) for each estimate.

I will open separate issues for the left.

Originally posted by @arunge in https://github.com/Pandora-IsoMemo/osteo-bior/issues/43#issuecomment-2077109882

[isomemo]

@arunge @CarloCocozza you should comment on this when you are feeling better ;-)

[CarloCocozza]

Hi @arunge , I have tested the plot production. Overall this works well. I just have to report a few things:

-there is an error in the mathematical annotation example: "Bayesian Estimated" ~ delta^~13*C ~ ("‰" - ~ "VPDB") should be "Bayesian Estimated" ~ delta^~13~C ~ ("‰" - ~ "VPDB") otherwise the C will be superscript as well. -I may need mathematical annotation also in the legend names, which as we discussed, should be done by saving the original model name with a new name. -I did not understand how to remove the secondary axis if I do not need it anymore -There should be the same options for the secondary axis as in the y-axis (size, colour, font, etc.). Moreover, here is also needed the mathematical annotation. -discussion as in #55 about single measurements gaps (i.e. possibility to manually add single dots)

Regarding the Mcp package (#49 ) I do not understand how to tell the package which model to consider (I refer to OsteoBioR model, not Mcp model).

[arunge]

With version 24.10.0 on OsteoBioR beta I pushed following of your notes from above:

• [x] there is an error in the mathematical annotation example: "Bayesian Estimated" ~ delta^~13*C ~ ("‰" - ~ "VPDB") should be "Bayesian Estimated" ~ delta^~13~C ~ ("‰" - ~ "VPDB") otherwise the C will be superscript as well.
• [x] There should be the same options for the secondary axis as in the y-axis (size, colour, font, etc.). Moreover, here is also needed the mathematical annotation.

Regarding the next points:

• I did not understand how to remove the secondary axis if I do not need it anymore

Please just remove the text from the input 'Add a new secondary axis' and press 'Apply'. This removes the 2nd y axis. Currently, this only works with the beta version. I will push the changes to the main when we are done here.

Regarding the Mcp package (#49 ) I do not understand how to tell the package which model to consider (I refer to OsteoBioR model, not Mcp model).

Please, check here.

-discussion as in #55 about single measurements gaps (i.e. possibility to manually add single dots)

Please, check here.

• I may need mathematical annotation also in the legend names, which as we discussed, should be done by saving the original model name with a new name.

This will not be possible that easily. I cannot use mathematical annotations as model names, here only text is possible. Than we must develop a new user inputs to update the legend texts when creating the plot. This step must be planned first, and needs some more time.