handle all calls to metadata when not provided

[Kdreval]

Ok this is ready to be looked at, substitutes all the metadata calls with the data

[Kdreval]

This is ready for re-review

[vladimirsouza]

You need to run devtools::document()

[vladimirsouza]

This could be my installation. To make this branch work, we have to install your kdreval-helpers-setup branch (not pushed to GAMBLR.helpers main yet) before it, right?

#get lymphgen colours
lymphgen_colours = get_gambl_colours(classification = "lymphgen")

#build plot
ashm_multi_rainbow_plot(regions_to_display = c("BCL2-TSS",
                                               "MYC-TSS",
                                               "SGK1-TSS",
                                               "IGL"),
                        custom_colours = lymphgen_colours,
                        seq_type = "genome")
Error in `arrange()` at GAMBLR.viz/R/ashm_multi_rainbow_plot.R:55:4:
ℹ In argument: `..1 = pathology_rank`.
Caused by error:
! object 'pathology_rank' not found
Run `rlang::last_trace()` to see where the error occurred.

The error happens in the line

meta_arranged = arrange(metadata, pathology_rank, lymphgen)

It looks like there is no pathology_rank column in the returned data.frame from GAMBLR.helpers::handle_metadata():

any( names(metadata) == "pathology_rank" )
# [1] FALSE

[Kdreval]

Thanks for reporting, the pathology_rank is not part of the gambl_metadata but I will add it now

[Kdreval]

Ok the pathology_rank column was added as is now part of the PR in that repo

[Kdreval]

You need to run devtools::document()

Can confirm it was run. No files were modified in order to push to remote, so everything should be in place ✅ Maybe you mentioned something that is not in sync?

[vladimirsouza]

Ok the pathology_rank column was added as is now part of the PR in that repo

I updated my local copy of your GAMBLR.helpers branch with git pull and it said Already up to date.. Have you pushed your commit?

[Kdreval]

Yes. Don't forget to pull the master from GAMBLR.data and install it, too

[Kdreval]

This is the commit you should make sure to be up-to-date with. It is on master already

[vladimirsouza]

ashm_multi_rainbow_plot is working perfectly now.

[Kdreval]

Thanks for confirming, great news! :scienceparrot:

[vladimirsouza]

Nothing important, but when I run devtools::document() on this branch, this files are modified.

[vladimirsouza]

For me, the branch can be merged.