This PR includes a variety of hotfixes and updates to existing functions. Including;
assign_cn_to_ssm now takes this_seq_type parameter.
get_cn_segments now has support for flat files.
prettyOncoplot can now deal with silent mutations.
More examples added to test_functions.R.
Improved instructions on how to run remote (README).
Supressing annoying warning messages from readr.
Updates to fancy_v_count so that it correctly calls assign_cn_to_ssm.
Updates to the config (redundant line from get_gene_expression update).
Hotfix for fancy_x_plot functions that threw unnecessary writing messages.
Adding SSM thematic vignette.
Improvements to ashm_rainbow_plot (fixing fill, margins, axis titles, ticks, etc.).
Added new thematic vignette (CN/SV), in progress...
For more info, please see the commit messages below.
This branch was recently merged with the current master (22/11). Many merge conflicts were flagged, and even though the majority of these conflicts could be resolved automatically, a handful had to be resolved manually.
I have also tested this branch using the examples available in test_functions.R. The functions listed in this script runs without errors and are producing the expected outputs. With that being said, I would highly recommend at least one additional tester to also confirm this given the number of merge conflicts and updates to commonly used GAMBLR functions, and perhaps other examples that are not (yet) represented in test_functions.R
After this PR has been approved, I will close the corresponding issues on this repo.
If this PR should still be active upon my return from Sweden, I have some additional improvements that I am currently working on. But these could also very well be on a future PR.
This PR includes a variety of hotfixes and updates to existing functions. Including;
assign_cn_to_ssmnow takesthis_seq_typeparameter.get_cn_segmentsnow has support for flat files.prettyOncoplotcan now deal with silent mutations.test_functions.R.readr.fancy_v_countso that it correctly callsassign_cn_to_ssm.get_gene_expressionupdate).fancy_x_plotfunctions that threw unnecessary writing messages.ashm_rainbow_plot(fixing fill, margins, axis titles, ticks, etc.).For more info, please see the commit messages below.
This branch was recently merged with the current master (22/11). Many merge conflicts were flagged, and even though the majority of these conflicts could be resolved automatically, a handful had to be resolved manually.
I have also tested this branch using the examples available in
test_functions.R. The functions listed in this script runs without errors and are producing the expected outputs. With that being said, I would highly recommend at least one additional tester to also confirm this given the number of merge conflicts and updates to commonly used GAMBLR functions, and perhaps other examples that are not (yet) represented in test_functions.RAfter this PR has been approved, I will close the corresponding issues on this repo.
If this PR should still be active upon my return from Sweden, I have some additional improvements that I am currently working on. But these could also very well be on a future PR.
Let me know if there are any questions.
Thanks,