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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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Fix function code and examples #25

Closed vladimirsouza closed 6 months ago

vladimirsouza commented 7 months ago

Finally no errors! Screenshot from 2023-12-13 13-10-24

vladimirsouza commented 7 months ago

The changes in prettyRainfallPlot fix this warning message, but the function keeps returning the same plot:

> prettyRainfallPlot(this_sample_id = "DOHH-2",
+                    this_seq_type = "genome",
+                    zoom_in_region = "8:125252796-135253201",
+                    label_sv = TRUE)
MAF df or path to custom MAF file was not provided, getting SSM using GAMBLR ...
Using the bundled SSM calls (.maf) calls in GAMBLR.data...
Using the bundled metadata in GAMBLR.data...
Getting combined manta + GRIDSS SVs using GAMBLR ...
Using the bundled Manta SV (.bedpe) calls in GAMBLR.data...
Using the bundled metadata in GAMBLR.data...
Warning message:
There was 1 warning in `dplyr::filter()`.
ℹ In argument: `if (...) NULL`.
ℹ In group 1: `fusion = "IGH-MYC"` and `chromosomeN = chrom1`.
Caused by warning in `if (grepl("1", chromosomeN)) ...`:
! the condition has length > 1 and only the first element will be used
vladimirsouza commented 6 months ago

The changes in the commit Fix warning message when getting manta results are to fix the same issue in R/fancy_sv_sizedens.R described above.