Add VAF vs depth plots

[FerriolCalvet]

Add the plots for the relationship between depth and a number of quantitative metrics:

• VAF (depth per site)
• Mutation density (with depth value from the mutation density file & also with average depth per gene)
  • Different flavours: all, protein affecting, non protein affecting
• Omega (average depth per gene)
• OncodriveFML (average depth per gene)

We should start with the plots for VAF and mutation density, since they are the simplest ones, and then it would be great to do it for the other metrics at the level of the gene where instead of using the depths per position we should load the information from the average depth in each of those genes.

For each of these metrics, we should generate this scatterplot and then add on top of it the hyperbolic curves of 1/depth, 2/depth up to N/depth for Ns up to a reasonable number.

It would be good to also get some counts on how many of the mutations/mutation density values follow these curves.

[efigb]

• Add VAF QC plot on distribution of VAF_AM vs VAF from deepCSA output directory: /mutations/clean_somatic/all_samples.somatic.mutations.tsv (could also be added for germline as well)

df_long = somatic_maf.melt(value_vars=["VAF", "VAF_AM"], 
                           var_name="VAF_type", 
                           value_name="VAF_value")

fig, ax = plt.subplots(figsize=(5, 4))
sns.histplot(data=df_long, x="VAF_value", hue="VAF_type", 
             ax=ax, palette=["dodgerblue", "orange"],
             log_scale=True, element="step")

plt.show()

[FerriolCalvet]

Bet if you want some guidance, I would add it to the python script that is being used for the plot mutation specific QCs where I think there are already some plots for VAF and VAF_AM

[FerriolCalvet]

here:

1. open a new branch as well
2. Add your code to this python script: https://github.com/bbglab/deepCSA/blob/dev/bin/plot_qc_mutations_vaf.py
   Create a function with the code and make sure that the plots are then properly stored.
3. Open a PR to merge the changes

[efigb]

here:

1. open a new branch as well
2. Add your code to this python script: https://github.com/bbglab/deepCSA/blob/dev/bin/plot_qc_mutations_vaf.py
   Create a function with the code and make sure that the plots are then properly stored.
3. Open a PR to merge the changes

PR to merge into dev done!