Squashed commit of the following:

commit fe050d47
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Fri Jul 31 12:57:11 2020 +0300

    Include usage instruction inside function body

    Include usage instruction inside function body, so on typing just the function name to display the R code, the instructions will appear.
    Also stated things clearly in the T&C

commit fedbca4a
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Thu Jul 30 12:50:20 2020 +0300

    Updates

    1. Improve readability
    2. Manage differing lengths of breaks and labels.

commit fb32fb91
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Thu Jul 30 12:43:20 2020 +0300

    skip.steps works as expected

    skip.steps = 1, now skips 1 observation.

commit 00a8bbcf
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Thu Jul 30 12:32:16 2020 +0300

    add script to calculate breaks for axes in ggplot2

    calculates breaks and labels for axes in ggplot2 with user defined gaps

IsolateCanonicalVariant.R

+# Installing dependencies
+dependencies <- c("stringi", "doParallel")
+missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
+if(length(missing_packages)) install.packages(missing_packages) 
+rm(missing_packages,dependencies)
+
+IsolateCanonicalVariant <- function (AAchangeAnnotations){
 # #<---------------------------->
-# # Please include this section when distributing and/or using this code. 
-# # Please read and abide by the terms of the included LICENSE
+# # You must include this section when:
+# # Distributing, Using and/or Modifying this code. 
+# # Please read and abide by the terms of the included LICENSE.
+# # Copyright 2020, Deepankar Chakroborty, All rights reserved.
 # #
 # #  Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
 # #  Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
 # #  License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
-# #
+# #<---------------------------->
+
+
 # #  PURPOSE:
 # #  From a given vector of annotations for a particular DNA change
 # #  this function selects the canonical variant (if present)
 # #  by cross referencing the MANE Select and RefSeq Select sets.
-# #
-# #  Logic flow:
+
+# #  LOGIC FLOW:
 # #  - If there is only one annotation; that is selected
 # #  - If canonical transcript is not found in MANE Select + RefSeq select 
 # #     or a matching transcript ID is not found in the annotation then;
 # #     The mutation with to the the highest position (residue number) is selected.
 # #  - If a match for canonical isoform is found then; 
 # #        that particular mutation is selected
-# #
-# #<---------------------------->
   
-# Installing dependencies
-dependencies <- c("stringi", "doParallel")
-missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
-if(length(missing_packages)) install.packages(missing_packages) 
-rm(missing_packages,dependencies)
-
-IsolateCanonicalVariant <- function (AAchangeAnnotations){
   # importing resources
   library(doParallel)
   refseq <- readRDS(url("https://gitlab.utu.fi/deecha/shared_scripts/-/raw/master/asset/RefSeqSelect_Gene_Transcript.RDS"),"rb")

MutSiteFind.R

+# Installing missing dependencies
+dependencies <- c("stringi")
+missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
+if(length(missing_packages)) install.packages(missing_packages) 
+rm(missing_packages,dependencies)
+
+MutSiteFind <- function(MutationColumn){
 # #<---------------------------->
-# # Please include this section when distributing and/or using this code. 
-# # Please read and abide by the terms of the included LICENSE
+# # You must include this section when:
+# # Distributing, Using and/or Modifying this code. 
+# # Please read and abide by the terms of the included LICENSE.
+# # Copyright 2020, Deepankar Chakroborty, All rights reserved.
 # #
 # #  Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
 # #  Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
 # #  License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
-# #
+# #<---------------------------->
+
+
 # #  PURPOSE:
 # #  For a given vector of amino acid changes like A123T, V256F, E746_A750del
 # #  this function returns c(123, 256, 746) as amino acid positions of
 # #  the mutated residue. 
-# #     In case of indels, it doesn't return the range!! (returns only the start position)
-# #
-# #<---------------------------->
+# #     In case of indels, it doesn't return the range!! 
+# #        (i.e. returns only the start position)
 
-dependencies <- c("stringi")
-missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
-if(length(missing_packages)) install.packages(missing_packages) 
-rm(missing_packages,dependencies)
 
-MutSiteFind <- function(MutationColumn){
   return(unlist(x = stringi::stri_extract_first_regex(str = MutationColumn,pattern = "[[:digit:]]+"), use.names = F))
 }
 

ggplotBreaks.R

+ggplotBreaks <- function(range,tick,skip.steps=0){
 # #<---------------------------->
-# # Please include this section when distributing and/or using this code. 
-# # Please read and abide by the terms of the included LICENSE
+# # You must include this section when:
+# # Distributing, Using and/or Modifying this code. 
+# # Please read and abide by the terms of the included LICENSE.
+# # Copyright 2020, Deepankar Chakroborty, All rights reserved.
 # #
 # #  Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
 # #  Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
 # #  License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
-# #
+# #<---------------------------->
+
+
 # #  PURPOSE:
 # #  Returns a list of vectors containing breaks and labels 
 # # for a continuous variable mapped to one of the axes for use with ggplot2
@@ -20,12 +25,8 @@
 # #     0  10  20  30  40  50  60  70  80  90 100 110 120 130 140 150
 # # 
 # #  $labels
-# #    "0"  " "  "20"  " "  "40"  " "  "60"  " "  "80"  " "  "100"  " "
-# #    "120"  " "  "140"  " "
-# #
-# #<---------------------------->
+# #    "0"  " "  "20"  " "  "40"  " "  "60"  " "  "80"  " "  "100"  " "  "120"  " "  "140"  " "
 
-ggplotBreaks <- function(range,tick,skip.steps=0){
   if (length(range) != 2){
     stop("Correct format for: range = c(min_value,max_value)")
   }

unparalogMutations.R

+# Installing missing dependencies
+dependencies <- c("stringi", "progress")
+missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
+if(length(missing_packages)) install.packages(missing_packages)
+rm(missing_packages,dependencies)
+
+unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",", GeneColName , AnnotationColName ){
 # #<---------------------------->
-# # Please include this section when distributing and/or using this code. 
-# # Please read and abide by the terms of the included LICENSE
+# # You must include this section when:
+# # Distributing, Using and/or Modifying this code. 
+# # Please read and abide by the terms of the included LICENSE.
+# # Copyright 2020, Deepankar Chakroborty, All rights reserved.
 # #
 # #  Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
 # #  Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
 # #  License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
-# #
+# #<---------------------------->
+
+
 # #  PURPOSE:
 # #  In the gene column in your SNV annotation if you see something like:
 # #  e.g. PRAMEF7;PRAMEF8  OR  PRAMEF7,PRAMEF8
 # #       then your mutations annotations have gene paralogs.
 # #  This script aims to de-couple those paralogs into individual their rows.
 # #
-# ------------------------ 
    
-### Info on what to pass as the function parameters:
+# # INFO on what to pass as the function parameters:
 # Assign correct paralog_separator found in the gene column of your SNV annotations # e.g. if the Gene column has entries like PRAMEF7;PRAMEF8 
 # then the paralog_separator is ";" 
 # or set it to whatever separator is used by your SNV annotation software.
@@ -29,13 +39,6 @@
 
 # <--------------->
    
-# Installing missing dependencies
-dependencies <- c("stringi", "progress")
-missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
-if(length(missing_packages)) install.packages(missing_packages)
-rm(missing_packages,dependencies)
-
-unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",", GeneColName , AnnotationColName ){
    # Sanity checks
    check_paralog_sep <- !any(stringi::stri_detect_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
    check_annotation_sep <- !any(stringi::stri_detect_fixed(str =  DATA$AAChange.refGene, pattern = annotation_separator))