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morinlab / GAMBLR.viz

Collection of functions to make plots for Genomic Analysis of Mature B-cell Lymphomas in R
https://morinlab.github.io/GAMBLR.viz/
MIT License
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`fancy_v_count` doesn't work when GAMBLR.results is loaded #18

Closed vladimirsouza closed 7 months ago

vladimirsouza commented 7 months ago 
> library(GAMBLR.results)
> fancy_v_count(this_sample_id = "DOHH-2")
This function only works with matched samples for now                                                                                                          
trying to find output from: battenberg                                                                                                                         
looking for flatfile: 
Error in if (!file.exists(battenberg_file)) { : 
  argument is of length zero

This is because assign_cn_to_ssm is used internally, which calls get_sample_wildcards to try to find the battenberg file path. However, get_sample_wildcards doesn’t work with unmatched samples.

fancy_v_count works fine if using the bundled data (GAMBLR.data).

vladimirsouza commented 7 months ago

Other functions that use assign_cn_to_ssm and might get the same problem:

comp_report
fancy_v_count
fancy_v_chrcount
fancy_circos_plot
copy_number_vaf_plot
fancy_v_sizedis
fancy_snv_chrdistplot
fancy_ideogram
mattssca commented 7 months ago

All the mentioned plotting function will have their internal call of assign_cn_to_ssm replaced with appropriate GAMBLR functions for retrieving the required plot data. I will self-assign this issue and provide the required update when ready.