Add refs

[mblue9]

I added some refs here if you want them for voom, edger test methods, epic, llsr, ggplot2.
Guess tidyheatmap can't be added as tidybulk doesn't use it under the hood?

[stemangiola]

Cool, I need to intercept this pull request to add the track of those reference in the methods as well (unless you know how to do it).

e.g.

But if you prefer to not go as deep I can do it no prob.

Guess tidyheatmap can't be added as tidybulk doesn't use it under the hood?

I though about that XD, we could build a wrapper for tidyHeatmap, so to be able to call it without specifying sample, transcript, count (as we do for any other method). But let's think about that whether it's overkill.

[mblue9]

I am happy to have a go at adding tomorrow but I'm not sure everywhere they need to be added so you will need to check 😄

[mblue9]

Ok tried to add, could you check when you can.

[stemangiola]

Ok tried to add, could you check when you can.

Looks good to me! For deconvolution you brought inside the when assignments, it should work.

Have to tested by any chance whether the bibliography is ultimately what you expect?

[stemangiola]

If I manage I might push this change into the new Bioconductor release (going public today)

[mblue9]

I'll have a look at testing this now...

[mblue9]

Tested running the DE methods separately and together and the refs seem to get added fine.

But get_bibliography does not work with the changes here to the deconvolution methods e.g.

 > get_bibliography(epic_res)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘get_bibliography’ for signature ‘"tbl_df"’

But it doesn't seem like it worked before these changes for the deconvolution methods as installing tidybulk from Bioc devel (v 1.1.9) I get same error with method = "get", is only supposed to work with method="add"?

> BRCA_tidy <-
  BRCA %>%
   tidybulk(patient, transcript, count)
> res <- BRCA_tidy %>%
  deconvolve_cellularity(action="get", cores=2)
> get_bibliography(res)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘get_bibliography’ for signature ‘"tbl_df"’

Using method="add"

> res <- BRCA_tidy %>%
   deconvolve_cellularity(cores=2)
> get_bibliography(res)

@article{wickham2019welcome,
  title={Welcome to the Tidyverse},
  author={Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang, Winston and McGowan, Lucy D'Agostino and Francois, Romain and Grolemund, Garrett and Hayes, Alex and Henry, Lionel and Hester, Jim and others},
  journal={Journal of Open Source Software},
  volume={4},
  number={43},
  pages={1686},
  year={2019}
	}

Cibersort ref is not added.

[stemangiola]

is only supposed to work with method="add"?

No. I will have a look.

[stemangiola]

is only supposed to work with method="add"

[EDIT[

No. Now works in all scenarios. With the new pull request.