Merge branch 'JRaviLab:main' into rworkflow

.github/.gitignore

@@ -1 +1,3 @@
 *.html
+
+/.quarto/

.github/CONTRIBUTING.md

@@ -5,42 +5,87 @@ For a detailed discussion on contributing to this and other tidyverse packages,
 
 ## Fixing typos
 
-You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file. 
-This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file. 
+You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file.
+This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file.
 You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.
 
 ## Bigger changes
 
-If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed. 
-If you’ve found a bug, please file an issue that illustrates the bug with a minimal 
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed.
+If you’ve found a bug, please file an issue that illustrates the bug with a minimal
 [reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
 See our guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.
 
 ### Pull request process
 
-*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("JRaviLab/MolEvolvR", fork = TRUE)`.
+- Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis`.
 
-*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
-    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
-*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+- Install and load the `usethis` package with:
 
-*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
-    The title of your PR should briefly describe the change.
-    The body of your PR should contain `Fixes #issue-number`.
+  ```
+  install.packages("usethis")
 
-*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+  library("usethis")
+  ```
+
+- Clone and fork the MolEvolvR package using:
+  ```
+  usethis::create_from_github("JRaviLab/MolEvolvR", fork = TRUE)
+  ```
+- Install BiocManager from Bioconductor:
+
+  ```
+  if (!require("BiocManager", quietly = TRUE))
+      install.packages("BiocManager")
+  BiocManager::install(version = "3.19")
+  ```
+
+- Install other development dependencies and then ensure that the package passes R CMD check using `devtools`:
+
+  ```
+  install.packages("devtools")
+
+  library("devtools")
+
+  devtools::install_dev_deps()
+
+  devtools::check()
+  ```
+
+  _If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing._
+
+- Create a Git branch for your pull request (PR). We recommend using:
+
+  ```
+  usethis::pr_init("brief-description-of-change")
+  ```
+
+- Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+  The title of your PR should briefly describe the change.
+  The body of your PR should contain `Fixes #issue-number`.
+
+<!-- *  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>. -->
+
+<!-- No NEWS.md file exists at the moment. Suggest restoring this line when the file exists to avoid a y confusion.-->
 
 ### Code style
 
-*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
-    You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
-
-*   Lint Your Code: Ensure your code adheres to our style guidelines by using [lintr](https://lintr.r-lib.org/): `lintr::lint("path/to/your/file.R")`
+- New code should follow the tidyverse [style guide](https://style.tidyverse.org).
+  You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.
+- Lint Your Code: Ensure your code adheres to our style guidelines by using [lintr](https://lintr.r-lib.org/):
+
+  ```
+  install.packages("lintr")
+
+  library("lintr")
+
+  lintr::lint("path/to/your/file.R")
+  ```
 
-*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.  
+- We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.
 
-*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
-   Contributions with test cases included are easier to accept.  
+- We use [testthat](https://cran.r-project.org/package=testthat) for unit tests.
+  Contributions with test cases included are easier to accept.
 
 ## Code of Conduct
 

NAMESPACE

@@ -1,67 +1,63 @@
 # Generated by roxygen2: do not edit by hand
 
-export(BinaryDomainNetwork)
 export(GCA2Lineage)
-export(GenContextNetwork)
 export(IPG2Lineage)
-export(RepresentativeAccNums)
 export(acc2FA)
 export(acc2Lineage)
 export(acc2fa)
 export(addLeaves2Alignment)
 export(addLineage)
 export(addName)
 export(addTaxID)
-export(add_leaves)
-export(add_name)
-export(advanced_opts2est_walltime)
 export(alignFasta)
-export(assign_job_queue)
+export(assignJobQueue)
+export(calculateEstimatedWallTimeFromOpts)
+export(calculateProcessRuntime)
 export(cleanClusters)
 export(cleanDomainArchitecture)
 export(cleanGeneDescription)
 export(cleanGenomicContext)
 export(cleanLineage)
 export(cleanSpecies)
-export(combine_files)
-export(combine_full)
-export(combine_ipr)
+export(combineFiles)
+export(combineFullAnalysis)
+export(combineIPR)
 export(condenseRepeatedDomains)
 export(convert2TitleCase)
 export(convertAlignment2FA)
 export(convertAlignment2Trees)
 export(convertFA2Tree)
-export(convert_aln2fa)
 export(countByColumn)
+export(createBinaryDomainNetwork)
+export(createDomainNetwork)
 export(createFA2Tree)
+export(createGenomicContextNetwork)
 export(createJobResultsURL)
 export(createJobStatusEmailMessage)
+export(createLineageLookup)
+export(createMSA_Kalign)
+export(createMSA_PDF)
+export(createRepresentativeAccNum)
+export(createUndirectedGenomicContextNetwork)
 export(createWordCloud2Element)
 export(createWordCloudElement)
-export(create_lineage_lookup)
-export(domain_network)
 export(downloadAssemblySummary)
 export(efetchIPG)
 export(extractAccNum)
 export(filterByDomains)
 export(filterByFrequency)
 export(findParalogs)
-export(find_top_acc)
 export(formatJobArgumentsHTML)
-export(gc_undirected_network)
 export(generateAllAlignments2FA)
-export(generate_all_aln2fa)
-export(generate_msa)
-export(get_accnums_from_fasta_file)
-export(get_proc_medians)
-export(get_proc_weights)
-export(ipr2viz)
-export(ipr2viz_web)
-export(make_opts2procs)
+export(getAccNumFromFA)
+export(getProcessRuntimeWeights)
+export(getTopAccByLinDomArch)
 export(mapAcc2Name)
-export(map_acc2name)
-export(map_advanced_opts2procs)
-export(msa_pdf)
+export(mapAdvOption2Process)
+export(mapOption2Process)
+export(plotEstimatedWallTimes)
+export(plotIPR2Viz)
+export(plotIPR2VizWeb)
 export(plotLineageDA)
 export(plotLineageDomainRepeats)
 export(plotLineageHeatmap)
@@ -72,7 +68,6 @@ export(plotStackedLineage)
 export(plotSunburst)
 export(plotTreemap)
 export(plotUpSet)
-export(plot_estimated_walltimes)
 export(prepareColumnParams)
 export(prepareSingleColumnParams)
 export(proteinAcc2TaxID)
@@ -83,28 +78,27 @@ export(removeTails)
 export(renameFA)
 export(rename_fasta)
 export(replaceQuestionMarks)
-export(reveql)
-export(reverse_operon)
-export(run_deltablast)
-export(run_rpsblast)
+export(reverseOperonSeq)
+export(runDeltaBlast)
+export(runRPSBlast)
 export(selectLongestDuplicate)
 export(sendJobStatusEmail)
 export(shortenLineage)
 export(sinkReset)
+export(straightenOperonSeq)
 export(summarizeByLineage)
 export(summarizeDomArch)
 export(summarizeDomArch_ByLineage)
 export(summarizeGenContext)
 export(summarizeGenContext_ByDomArchLineage)
 export(summarizeGenContext_ByLineage)
-export(theme_genes2)
-export(to_titlecase)
+export(themeGenes2)
 export(totalGenContextOrDomArchCounts)
 export(validateCountDF)
 export(wordcloud3)
-export(write.MsaAAMultipleAlignment)
-export(write_proc_medians_table)
-export(write_proc_medians_yml)
+export(writeMSA_AA2FA)
+export(writeProcessRuntime2TSV)
+export(writeProcessRuntime2YML)
 importFrom(Biostrings,AAStringSet)
 importFrom(Biostrings,readAAStringSet)
 importFrom(Biostrings,toString)

R/CHANGED-pre-msa-tree.R

@@ -54,7 +54,7 @@ convert2TitleCase <- function(x, y = " ") {
 ################################
 ## Function to add leaves to an alignment file
 ## !! Add DA to leaves?
-#' Adding Leaves to an alignment file w/ accessions
+#' addLeaves2Alignment
 #'
 #' @author Janani Ravi
 #' @keywords alignment, accnum, leaves, lineage, species
@@ -178,7 +178,7 @@ addLeaves2Alignment <- function(aln_file = "",
 }
 
 
-#' Add Name
+#' addName
 #'
 #' @author Samuel Chen, Janani Ravi
 #' @description This function adds a new 'Name' column that is comprised of components from
@@ -252,7 +252,7 @@ addName <- function(data,
 
 ################################
 ## Function to convert alignment 'aln' to fasta format for MSA + Tree
-#' Adding Leaves to an alignment file w/ accessions
+#' convertAlignment2FA
 #'
 #' @author Janani Ravi
 #' @keywords alignment, accnum, leaves, lineage, species
@@ -320,6 +320,9 @@ convertAlignment2FA <- function(aln_file = "",
     return(fasta)
 }
 
+#' mapAcc2Name
+#' 
+#' @description
 #' Default renameFA() replacement function. Maps an accession number to its name
 #'
 #' @param line The line of a fasta file starting with '>'
@@ -382,6 +385,9 @@ renameFA <- function(fa_path, outpath,
 
 ################################
 ## generateAllAlignments2FA
+#' generateAllAlignments2FA
+#' 
+#' @description 
 #' Adding Leaves to an alignment file w/ accessions
 #'
 #' @keywords alignment, accnum, leaves, lineage, species
@@ -441,10 +447,11 @@ generateAllAlignments2FA <- function(aln_path = here("data/rawdata_aln/"),
 
 # accessions <- c("P12345","Q9UHC1","O15530","Q14624","P0DTD1")
 # accessions <- rep("ANY95992.1", 201)
-#' acc2FA converts protein accession numbers to a fasta format.
+#' acc2FA 
 #'
 #' @description
-#' Resulting fasta file is written to the outpath.
+#' converts protein accession numbers to a fasta format. Resulting 
+#' fasta file is written to the outpath.
 #'
 #' @author Samuel Chen, Janani Ravi
 #' @keywords accnum, fasta
@@ -539,6 +546,9 @@ acc2FA <- function(accessions, outpath, plan = "sequential") {
     return(result)
 }
 
+#' createRepresentativeAccNum
+#' 
+#' @description
 #' Function to generate a vector of one Accession number per distinct observation from 'reduced' column
 #'
 #' @author Samuel Chen, Janani Ravi
@@ -556,7 +566,7 @@ acc2FA <- function(accessions, outpath, plan = "sequential") {
 #' @export
 #'
 #' @examples
-RepresentativeAccNums <- function(prot_data,
+createRepresentativeAccNum <- function(prot_data,
     reduced = "Lineage",
     accnum_col = "AccNum") {
     # Get Unique reduced column and then bind the AccNums back to get one AccNum per reduced column
@@ -585,6 +595,9 @@ RepresentativeAccNums <- function(prot_data,
     return(accessions)
 }
 
+#' alignFasta
+#' 
+#' @description
 #' Perform a Multiple Sequence Alignment on a FASTA file.
 #'
 #' @author Samuel Chen, Janani Ravi
@@ -610,12 +623,12 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
     )
 
     if (typeof(outpath) == "character") {
-        write.MsaAAMultipleAlignment(aligned, outpath)
+        writeMSA_AA2FA(aligned, outpath)
     }
     return(aligned)
 }
 
-#' Write MsaAAMultpleAlignment Objects as algined fasta sequence
+#' writeMSA_AA2FA
 #'
 #' @description
 #' MsaAAMultipleAlignment Objects are generated from calls to msaClustalOmega
@@ -632,7 +645,7 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
 #' @export
 #'
 #' @examples
-write.MsaAAMultipleAlignment <- function(alignment, outpath) {
+writeMSA_AA2FA <- function(alignment, outpath) {
     l <- length(rownames(alignment))
     fasta <- ""
     for (i in 1:l)
@@ -645,7 +658,7 @@ write.MsaAAMultipleAlignment <- function(alignment, outpath) {
     return(fasta)
 }
 
-#' Get accnums from fasta file
+#' getAccNumFromFA
 #'
 #' @param fasta_file
 #'
@@ -655,7 +668,7 @@ write.MsaAAMultipleAlignment <- function(alignment, outpath) {
 #' @export
 #'
 #' @examples
-get_accnums_from_fasta_file <- function(fasta_file) {
+getAccNumFromFA <- function(fasta_file) {
     txt <- read_file(fasta_file)
     accnums <- stringi::stri_extract_all_regex(fasta_file, "(?<=>)[\\w,.]+")[[1]]
     return(accnums)