hfuchs5 issues

Results 15 issues of


                                            hfuchs5

add unit testing for `add_point_mut()`

Add an example to vignette and/or docs that changes color palette of the ggcor or ggcomut plot

Could just be me, but maybe having an example of how to change the color palette for one of these plots would be helpful?

hackathon

unit testing for tbl_genomic(..., wide = T) needed

Mutation type matrix for ggoncoprint retained after `create_gene_binary()`

**What changes are proposed in this pull request?** Added var_class attribute option to `create_gene_binary()` which retains a long form of the mutation/fusion/cna files with variant_classification values. Haven't made official tests...

unit testing for mutation type attribute on `create_gene_binary()`

#335 #263

Update Docs to make sure new SV is canon-cbio has deprecated fusion files for sv

![image](https://github.com/MSKCC-Epi-Bio/gnomeR/assets/100386516/1251219d-f0b2-4548-a194-39bae1963a11) https://docs.cbioportal.org/file-formats/#structural-variant-data

Large datasets (1,000s of patients) takes a long time in `summarize_by_gene()`

Test the main package functions with different size maf files to better assess the problem.

Gb class internal func

**What changes are proposed in this pull request?** added a S3 object called "tbl_gene_binary" to allow functions to identify if data is the proper format, updated many functions to deal...

future

Allow users to select specific genes in ggcor (or add example of preselecting genes)

For example, gene correlations – user gets to pick which genes to correlate (not sure what the current selection process is)

Create a vignette for copy number data

From Caroline: I’ve been considering working on these sorts of functions/smoothing out this pipeline for my own personal use. Happy to share when complete if they belong in gnomeR or...

hackathon