Refactored function names in msa.R | networks_domarch.R | networks_gencontext.R

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)
@@ -30,31 +28,33 @@ export(convertAlignment2FA)
 export(convertAlignment2Trees)
 export(convertFA2Tree)
 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(domain_network)
 export(downloadAssemblySummary)
 export(efetchIPG)
 export(extractAccNum)
 export(filterByDomains)
 export(filterByFrequency)
 export(findParalogs)
 export(formatJobArgumentsHTML)
-export(gc_undirected_network)
 export(generateAllAlignments2FA)
-export(generate_msa)
 export(getAccNumFromFA)
 export(getProcessRuntimeWeights)
 export(getTopAccByLinDomArch)
 export(mapAcc2Name)
 export(mapAdvOption2Process)
 export(mapOption2Process)
-export(msa_pdf)
 export(plotEstimatedWallTimes)
 export(plotIPR2Viz)
 export(plotIPR2VizWeb)

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")
@@ -196,12 +196,12 @@ msa_pdf <- function(fasta_path, out_path = NULL,
 #' @export
 #'
 #' @examples
-generate_msa <- function(fa_file = "", outfile = "") {
-  prot_aa <- readAAStringSet(
-    fa_file,
-    format = "fasta"
-  )
-  prot_aa
+createMSA_Kalign <- function(fa_file = "", outfile = "") {
+    prot_aa <- readAAStringSet(
+        path = fa_file,
+        format = "fasta"
+    )
+    prot_aa
 
   ## Install kalign ?rMSA_INSTALL
   ## Messed up! Reimplement from kalign.R

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),

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.
@@ -37,9 +37,9 @@
 #'
 #' @examples
 #' \dontrun{
-#' domain_network(pspa)
+#' createUndirectedGenomicContextNetwork(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) {