[DOC] Function Inventory | add documentation w/ `docstring`

[the-mayer]

List of expected functions from molevol_scripts/R

Ensure all functions are present and accounted for. Use list depth to determine if function should be user facing (ie @export).

Import and combining input files

• [ ] scripts/convert_opinscls_tsv.R using
  • [ ] clean_clust_file
  • [ ] add_colnames (currently colnames.op_ins_cls and colnames.op_ins_cls.clus2table)
  • [ ] remove # rows and convert to columns w/ ID and clust_names
  • [ ] add_uniq_ids (to add GCA_ID, IPG, taxID columns based on AccNums)
  • [ ] add lineage

Cleanup

• [x] repeat2s

  • [x] repeated domains with (s)
  • [ ] alternative using map?

• [x] remove_tails

  • [x] by DomArch

• [x] remove_empty_rows

  • [x] by Species, DomArch, ClustName, GenContext

• [x] cleanup_clust

  • [ ] ! ClustName acts as DomArch?
  • [x] remove start and end '+'s
  • [x] domains_keep remove rows without query (reads query_domains, domains_keep)
  • [x] domains_rename (reads domains_rename)
  • [ ] ignored? (reads clustnames_ignore)
  • [x] repeat2s: repeated domains with (s)
  • [x] remove_tails
  • [x] remove empty rows?

• [x] cleanup_species

  • [ ] remove_empty rows (!change it to an alert about AccNums w/ no lineage/spp)
  • [x] removes special characters
  • [x] check if empty rows/taxIDs are because of server retrieval errors!

• [x] cleanup_domarch

  • [ ] ignored (reads domains_ignore)
  • [x] domains_keep remove rows without query (reads query_domains, domains_keep)
  • [x] replaced domains (reads domains_rename)
  • [x] remove start and end '+'s
  • [x] repeat2s: repeated domains with (s)
  • [x] remove empty rows?
  • [x] remove_tails

• [x] cleanup_gencontext

  • [x] reverse_operons
  • [x] repeat2s: repeated domains with (s)
  • [ ] remove empty rows? risky. many eukaryotes don't carry gencontexts!

• [x] add_leaves

  • [x] to_titlecase
  • [x] convert_aln2fa | convert_aln2tsv
  • [x] add_leaves | adding leaves based on AccNum, Lineage and Spp.
  • [ ] add DA to add_leaves too?
  • [ ] convert_accnum2fasta
  • [ ] filter_for_phylo

Summary stats

• [x] count_bycol
• [ ] generate_wordcount
  • [x] elements2words
  • [x] words2wc
  • [ ] filter_freq | mostly used within other functions
• [x] summary_bylin (for DA, GC)
  • [x] summ_DA_byLin
  • [x] summ_GC_byDALin
  • [x] summ_GC_byLin
• [x] summary_stats (for DA, GC)
  • [x] summ_DA
  • [x] summ_GC
• [x] total_counts
• [x] find_paralogs

Plotting

• [x] upset_plot
  • [ ] should depend on generate_wordcount
• [x] lineage_DA_plot
• [x] lineage_GC_plot
• [x] lineage_domain_repeats_plot??
• [x] wordcloud
• [ ] msa_tree
  • [ ] msa_pdf
  • [ ] phylotree?
• [x] prot_network
  • [x] by DA/domains
  • [x] by GC/DA
  • [x] subsets by prot/domain

[jananiravi]

@SunSummoner would you be interested in starting by generating a function map for the existing package? this will give us all an understanding of the dependent vs. independent functions & which of these need to be exported. Again, @the-mayer will be a good resource to check in regarding this.

[SunSummoner]

@SunSummoner would you be interested in starting by generating a function map for the existing package? this will give us all an understanding of the dependent vs. independent functions & which of these need to be exported. Again, @the-mayer will be a good resource to check in regarding this.

@jananiravi Yes, I will check in with him.

[awasyn]

Hi if this helps, you can have look at this function dependency graph i created with viznetwork. it is interactive html file. when opened it takes about 5s to load the components. select functions by id an zoom in to see it's dependency. you can also view all function dependencies at once. @jananiravi @the-mayer function_dependency_graph.zip

Some screenshots are added below for context.

[jananiravi]

@awasyn @SunSummoner, please remind us if there are open PRs for this automatic function dependency map generation. Thanks!

[SunSummoner]

@awasyn @SunSummoner, please remind us if there are open PRs for this automatic function dependency map generation. Thanks!

@jananiravi None from my side yet.

[awasyn]

@awasyn @SunSummoner, please remind us if there are open PRs for this automatic function dependency map generation. Thanks!

I just pushed a PR on this. I hesitated before because I was of the impression the task was assigned to another contributor. Sorry for the delay.