From 2057aa57a8101381adb9dffdd5a05e741843791e Mon Sep 17 00:00:00 2001
From: teddyCodex <samted.uche@gmail.com>
Date: Mon, 14 Oct 2024 19:00:08 +0100
Subject: [PATCH 1/4] refactor functions in multiple files

---
 R/msa.R                 | 10 +++++-----
 R/networks_domarch.R    |  8 ++++----
 R/networks_gencontext.R |  4 ++--
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/R/msa.R b/R/msa.R
index e56cc32c..4c48f323 100644
--- a/R/msa.R
+++ b/R/msa.R
@@ -24,7 +24,7 @@
 #############
 
 ## Sample Runs
-# msa_pdf(fasta_path="data/alns/pspb.gismo.fa" )#, out_path="data/msapdf")
+# createMSA_PDF(fasta_path="data/alns/pspb.gismo.fa" )#, out_path="data/msapdf")
 
 #########################################
 ## Generates MSA PDF from a Fasta file ##
@@ -34,7 +34,7 @@
 #' @description
 #' Generates a multiple sequence alignment from a fasta file
 #'
-#' msa_pdf is a function that reads a fasta file and generates a multiple sequence alignment as
+#' createMSA_PDF is a function that reads a fasta file and generates a multiple sequence alignment as
 #' a pdf
 #'
 #'
@@ -55,9 +55,9 @@
 #'
 #' @examples
 #' \dontrun{
-#' msa_pdf()
+#' createMSA_PDF()
 #' }
-msa_pdf <- function(fasta_path, out_path = NULL,
+createMSA_PDF <- function(fasta_path, out_path = NULL,
     lowerbound = NULL, upperbound = NULL) {
     ## SAMPLE ARGUMENTS to test run
     # fasta_path=here("../molevol_data/project_data/phage_defense/full_analysis_20210108/g3d.both_lin.gen.da_sub.fa")
@@ -196,7 +196,7 @@ msa_pdf <- function(fasta_path, out_path = NULL,
 #' @export
 #'
 #' @examples
-generate_msa <- function(fa_file = "", outfile = "") {
+createMSA_Kalign <- function(fa_file = "", outfile = "") {
     prot_aa <- readAAStringSet(
         path = fa_file,
         format = "fasta"
diff --git a/R/networks_domarch.R b/R/networks_domarch.R
index fea0a195..9215aa93 100755
--- a/R/networks_domarch.R
+++ b/R/networks_domarch.R
@@ -46,9 +46,9 @@
 #'
 #' @examples
 #' \dontrun{
-#' domain_network(pspa)
+#' createDomainNetwork(pspa)
 #' }
-domain_network <- function(prot, column = "DomArch", domains_of_interest, cutoff = 70, layout = "nice", query_color = adjustcolor("green", alpha.f = .5)) {
+createDomainNetwork <- function(prot, column = "DomArch", domains_of_interest, cutoff = 70, layout = "nice", query_color = adjustcolor("green", alpha.f = .5)) {
     # by domain networks or all, as required.
     tryCatch(
         {
@@ -250,9 +250,9 @@ domain_network <- function(prot, column = "DomArch", domains_of_interest, cutoff
 #'
 #' @examples
 #' \dontrun{
-#' domain_network(pspa)
+#' createDomainNetwork(pspa)
 #' }
-BinaryDomainNetwork <- function(prot, column = "DomArch", domains_of_interest, cutoff = 70,
+createBinaryDomainNetwork <- function(prot, column = "DomArch", domains_of_interest, cutoff = 70,
     layout = "nice", query_color = adjustcolor("yellow", alpha.f = .5),
     partner_color = adjustcolor("skyblue", alpha.f = .5),
     border_color = adjustcolor("grey", alpha.f = .8),
diff --git a/R/networks_gencontext.R b/R/networks_gencontext.R
index e0dd63da..7df6c270 100755
--- a/R/networks_gencontext.R
+++ b/R/networks_gencontext.R
@@ -39,7 +39,7 @@
 #' \dontrun{
 #' domain_network(pspa)
 #' }
-gc_undirected_network <- function(prot, column = "GenContext", domains_of_interest, cutoff_type = "Lineage", cutoff = 1, layout = "grid") {
+createUndirectedGenomicContextNetwork <- function(prot, column = "GenContext", domains_of_interest, cutoff_type = "Lineage", cutoff = 1, layout = "grid") {
     # by domain networks or all, as required.
     # ye is either all of prot.list or centered on one domain
 
@@ -146,7 +146,7 @@ gc_undirected_network <- function(prot, column = "GenContext", domains_of_intere
 #' \dontrun{
 #' gc_directed_network(pspa, column = "GenContex", cutoff = 55)
 #' }
-GenContextNetwork <- function(prot, domains_of_interest, column = "GenContext",
+createGenomicContextNetwork <- function(prot, domains_of_interest, column = "GenContext",
     cutoff = 40,
     layout = "grid",
     directed = TRUE) {

From b665a4dfd062f3a359cb907040cb8c384a23450c Mon Sep 17 00:00:00 2001
From: teddyCodex <samted.uche@gmail.com>
Date: Mon, 14 Oct 2024 19:03:29 +0100
Subject: [PATCH 2/4] Update NAMESPACE and .Rd files

---
 NAMESPACE                                         | 12 ++++++------
 ...ainNetwork.Rd => createBinaryDomainNetwork.Rd} |  8 ++++----
 man/{domain_network.Rd => createDomainNetwork.Rd} |  8 ++++----
 ...tNetwork.Rd => createGenomicContextNetwork.Rd} |  6 +++---
 man/{generate_msa.Rd => createMSA_Kalign.Rd}      |  6 +++---
 man/{msa_pdf.Rd => createMSA_PDF.Rd}              | 15 ++++++++++-----
 ...d => createUndirectedGenomicContextNetwork.Rd} |  6 +++---
 7 files changed, 33 insertions(+), 28 deletions(-)
 rename man/{BinaryDomainNetwork.Rd => createBinaryDomainNetwork.Rd} (92%)
 rename man/{domain_network.Rd => createDomainNetwork.Rd} (90%)
 rename man/{GenContextNetwork.Rd => createGenomicContextNetwork.Rd} (91%)
 rename man/{generate_msa.Rd => createMSA_Kalign.Rd} (70%)
 rename man/{msa_pdf.Rd => createMSA_PDF.Rd} (77%)
 rename man/{gc_undirected_network.Rd => createUndirectedGenomicContextNetwork.Rd} (90%)

diff --git a/NAMESPACE b/NAMESPACE
index fe4c23d6..4c05dc94 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,8 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(BinaryDomainNetwork)
 export(GCA2Lineage)
-export(GenContextNetwork)
 export(IPG2Lineage)
 export(acc2FA)
 export(acc2Lineage)
@@ -29,14 +27,19 @@ export(convertAlignment2FA)
 export(convertAlignment2Trees)
 export(convertFA2Tree)
 export(countByColumn)
+export(createBinaryDomainNetwork)
+export(createDomainNetwork)
 export(createFA2Tree)
+export(createGenomicContextNetwork)
 export(createJobResultsURL)
 export(createJobStatusEmailMessage)
+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)
@@ -44,9 +47,7 @@ export(filterByDomains)
 export(filterByFrequency)
 export(findParalogs)
 export(formatJobArgumentsHTML)
-export(gc_undirected_network)
 export(generateAllAlignments2FA)
-export(generate_msa)
 export(getAccNumFromFA)
 export(getTopAccByLinDomArch)
 export(get_proc_medians)
@@ -54,7 +55,6 @@ export(get_proc_weights)
 export(make_opts2procs)
 export(mapAcc2Name)
 export(map_advanced_opts2procs)
-export(msa_pdf)
 export(plotIPR2Viz)
 export(plotIPR2VizWeb)
 export(plotLineageDA)
diff --git a/man/BinaryDomainNetwork.Rd b/man/createBinaryDomainNetwork.Rd
similarity index 92%
rename from man/BinaryDomainNetwork.Rd
rename to man/createBinaryDomainNetwork.Rd
index bb7e2353..4f0bdc5a 100644
--- a/man/BinaryDomainNetwork.Rd
+++ b/man/createBinaryDomainNetwork.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/networks_domarch.R
-\name{BinaryDomainNetwork}
-\alias{BinaryDomainNetwork}
+\name{createBinaryDomainNetwork}
+\alias{createBinaryDomainNetwork}
 \title{Domain Network}
 \usage{
-BinaryDomainNetwork(
+createBinaryDomainNetwork(
   prot,
   column = "DomArch",
   domains_of_interest,
@@ -42,6 +42,6 @@ A network of domains is returned based on shared domain architectures.
 }
 \examples{
 \dontrun{
-domain_network(pspa)
+createDomainNetwork(pspa)
 }
 }
diff --git a/man/domain_network.Rd b/man/createDomainNetwork.Rd
similarity index 90%
rename from man/domain_network.Rd
rename to man/createDomainNetwork.Rd
index 528e4924..1588af17 100644
--- a/man/domain_network.Rd
+++ b/man/createDomainNetwork.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/networks_domarch.R
-\name{domain_network}
-\alias{domain_network}
+\name{createDomainNetwork}
+\alias{createDomainNetwork}
 \title{Domain Network}
 \usage{
-domain_network(
+createDomainNetwork(
   prot,
   column = "DomArch",
   domains_of_interest,
@@ -33,6 +33,6 @@ A network of domains is returned based on shared domain architectures.
 }
 \examples{
 \dontrun{
-domain_network(pspa)
+createDomainNetwork(pspa)
 }
 }
diff --git a/man/GenContextNetwork.Rd b/man/createGenomicContextNetwork.Rd
similarity index 91%
rename from man/GenContextNetwork.Rd
rename to man/createGenomicContextNetwork.Rd
index 2eeebbc5..ac6deb84 100644
--- a/man/GenContextNetwork.Rd
+++ b/man/createGenomicContextNetwork.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/networks_gencontext.R
-\name{GenContextNetwork}
-\alias{GenContextNetwork}
+\name{createGenomicContextNetwork}
+\alias{createGenomicContextNetwork}
 \title{Genomic Context Directed Network}
 \usage{
-GenContextNetwork(
+createGenomicContextNetwork(
   prot,
   domains_of_interest,
   column = "GenContext",
diff --git a/man/generate_msa.Rd b/man/createMSA_Kalign.Rd
similarity index 70%
rename from man/generate_msa.Rd
rename to man/createMSA_Kalign.Rd
index a68eb8b4..946f04ae 100644
--- a/man/generate_msa.Rd
+++ b/man/createMSA_Kalign.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/msa.R
-\name{generate_msa}
-\alias{generate_msa}
+\name{createMSA_Kalign}
+\alias{createMSA_Kalign}
 \title{Function to generate MSA using kalign}
 \usage{
-generate_msa(fa_file = "", outfile = "")
+createMSA_Kalign(fa_file = "", outfile = "")
 }
 \arguments{
 \item{outfile}{}
diff --git a/man/msa_pdf.Rd b/man/createMSA_PDF.Rd
similarity index 77%
rename from man/msa_pdf.Rd
rename to man/createMSA_PDF.Rd
index 4d5fed17..7cd7516a 100644
--- a/man/msa_pdf.Rd
+++ b/man/createMSA_PDF.Rd
@@ -1,10 +1,15 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/msa.R
-\name{msa_pdf}
-\alias{msa_pdf}
+\name{createMSA_PDF}
+\alias{createMSA_PDF}
 \title{Multiple Sequence Alignment}
 \usage{
-msa_pdf(fasta_path, out_path = NULL, lowerbound = NULL, upperbound = NULL)
+createMSA_PDF(
+  fasta_path,
+  out_path = NULL,
+  lowerbound = NULL,
+  upperbound = NULL
+)
 }
 \arguments{
 \item{fasta_path}{Character. The path location of the fasta file to be read.}
@@ -21,11 +26,11 @@ Default is NULL. If value is NULL, the entire multiple sequence alignment is pri
 \description{
 Generates a multiple sequence alignment from a fasta file
 
-msa_pdf is a function that reads a fasta file and generates a multiple sequence alignment as
+createMSA_PDF is a function that reads a fasta file and generates a multiple sequence alignment as
 a pdf
 }
 \examples{
 \dontrun{
-msa_pdf()
+createMSA_PDF()
 }
 }
diff --git a/man/gc_undirected_network.Rd b/man/createUndirectedGenomicContextNetwork.Rd
similarity index 90%
rename from man/gc_undirected_network.Rd
rename to man/createUndirectedGenomicContextNetwork.Rd
index 28cf1abb..d61c23df 100644
--- a/man/gc_undirected_network.Rd
+++ b/man/createUndirectedGenomicContextNetwork.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/networks_gencontext.R
-\name{gc_undirected_network}
-\alias{gc_undirected_network}
+\name{createUndirectedGenomicContextNetwork}
+\alias{createUndirectedGenomicContextNetwork}
 \title{Domain Network}
 \usage{
-gc_undirected_network(
+createUndirectedGenomicContextNetwork(
   prot,
   column = "GenContext",
   domains_of_interest,

From cdac9a3cc8a446596474fdc27892c2cc5fffbb3b Mon Sep 17 00:00:00 2001
From: David Mayer <david.mayer@cuanschutz.edu>
Date: Tue, 22 Oct 2024 15:27:32 -0600
Subject: [PATCH 3/4] let R sort NAMESPACE

---
 NAMESPACE | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 025f00cf..d91f16c9 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -34,9 +34,9 @@ export(createFA2Tree)
 export(createGenomicContextNetwork)
 export(createJobResultsURL)
 export(createJobStatusEmailMessage)
+export(createLineageLookup)
 export(createMSA_Kalign)
 export(createMSA_PDF)
-export(createLineageLookup)
 export(createRepresentativeAccNum)
 export(createUndirectedGenomicContextNetwork)
 export(createWordCloud2Element)
@@ -55,7 +55,6 @@ export(getTopAccByLinDomArch)
 export(mapAcc2Name)
 export(mapAdvOption2Process)
 export(mapOption2Process)
-export(msa_pdf)
 export(plotEstimatedWallTimes)
 export(plotIPR2Viz)
 export(plotIPR2VizWeb)

From 22504868261a7a56fa93c4889ac42a9becb66fff Mon Sep 17 00:00:00 2001
From: David Mayer <david.mayer@cuanschutz.edu>
Date: Tue, 22 Oct 2024 15:33:13 -0600
Subject: [PATCH 4/4] function/doc consistency

---
 R/networks_gencontext.R                      | 4 ++--
 man/createUndirectedGenomicContextNetwork.Rd | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/networks_gencontext.R b/R/networks_gencontext.R
index 7df6c270..ca1ef52d 100755
--- a/R/networks_gencontext.R
+++ b/R/networks_gencontext.R
@@ -8,7 +8,7 @@
 ## GC Undirected Network ##
 ###########################
 
-#' Domain Network
+#' createUndirectedGenomicContextNetwork
 #'
 #' @description
 #' This function creates a domain network from the 'DomArch' column.
@@ -37,7 +37,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' domain_network(pspa)
+#' createUndirectedGenomicContextNetwork(pspa)
 #' }
 createUndirectedGenomicContextNetwork <- function(prot, column = "GenContext", domains_of_interest, cutoff_type = "Lineage", cutoff = 1, layout = "grid") {
     # by domain networks or all, as required.
diff --git a/man/createUndirectedGenomicContextNetwork.Rd b/man/createUndirectedGenomicContextNetwork.Rd
index d61c23df..b74da141 100644
--- a/man/createUndirectedGenomicContextNetwork.Rd
+++ b/man/createUndirectedGenomicContextNetwork.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/networks_gencontext.R
 \name{createUndirectedGenomicContextNetwork}
 \alias{createUndirectedGenomicContextNetwork}
-\title{Domain Network}
+\title{createUndirectedGenomicContextNetwork}
 \usage{
 createUndirectedGenomicContextNetwork(
   prot,
@@ -35,6 +35,6 @@ A network of domains is returned based on shared domain architectures.
 }
 \examples{
 \dontrun{
-domain_network(pspa)
+createUndirectedGenomicContextNetwork(pspa)
 }
 }