Richard James Acton RichardJActon

## gist:a9c26878b7d0b302e51fbfc50230d237
$C3YlTaL7Gnbk9BJ1GvsliiDJqgBW9w1TWKjPdJuZ_jA

## proof.md

      
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                github_proof
              
          
    openpgp4fpr:5ee117648462e5a3610c19648e5defcfc3307916

  
## endpoint.json
{ "schemaVersion": 1, "label": "🥉 12", "message": "RSSPDC: Software Package", "color": "#E27022", "link": {"left": "https://gitlab.com/HDBI/data-management/checklists/"} }

## ggpseudo.txt
# ggpseudo syntax, ad hoc ggplot like pseudocode language I'm making up

# the data
# 1 column per row, these need to be expanded with repeats / missing
# values to represent the whole graphic
data = table(
	# columns
    `one or many peptides` = ["Study of one", "peptidomics"],

    # peptides / amino acids

## cutadapt_report_parser.pm
# cutadapt report parser
#######################################
sub reptParser {
	my $rept = $_[0];
	my %parsedRept;
	$rept =~ m/
		(?<head> [\S\s]* ===\sSummary\s===) \n+

		Total \s read \s pairs \s processed \: \s+
		(?<totalReadPairs>[\d,]+) \n \s+

## legendGen.R
#' legendGen
#' A function to generate colour legends
#' @param z.range a numeric vector of length 2
#' @param col a list with elements names low, mid and high with character vectors of length 1 containing colour names DEFAULT \code{list(low = 'lightgrey', mid = 'purple', high='green')}
#' @param nbins the number of bins in which to split the colours DEFAULT 20
#' @param nticks the number of axis ticks to display on the legend DEFAULT 5, setting to NA yeild just high and low tags
#' @param smooth boolean should the colour gadient be interpolated or left discrete? DEFAULT FALSE
#' @param title the title of the legend
#' @param tickFormatFunc a function to format the axis ticks e.g \code{function(x) {sprintf("%.e",x)}}
#' @param draw draw the function directly or return a grob for use in larger plots DEFAULT TRUE

## add lin and karnani cord tissue reference
# NB setwd to meffil/data-raw
library(devtools)
library(meffil)
library(minfi)
library(FlowSorted.CordTissueAndBlood.EPIC)

assign("reference.globals", new.env(), envir=environment())

load.env <- function(filename, env) {
	if (file.exists(filename))

## createAnnotationPackage.rn6.R
########################################################################################################################
## createAnnotationPackage.rn6.R
## created: 2019-02-04
## creator: Richard J. Acton
## ---------------------------------------------------------------------------------------------------------------------
## Annotation package creation for rn6.
########################################################################################################################

## F U N C T I O N S ###################################################################################################

## RtoUpSetWeb.R
# Libs
library(UpSetR)
library(jsonlite)

# Functions

# from: https://github.com/hms-dbmi/UpSetR/issues/85#issuecomment-327900647
fromListNamed <- function (input) {
	# Same as original fromList()...
	elements <- unique(unlist(input))
	# ggpseudo syntax, ad hoc ggplot like pseudocode language I'm making up

	# the data
	# 1 column per row, these need to be expanded with repeats / missing
	# values to represent the whole graphic
	data = table(
	# columns
	`one or many peptides` = ["Study of one", "peptidomics"],

	# peptides / amino acids
	# cutadapt report parser
	#######################################
	sub reptParser {
	my $rept = $_[0];
	my %parsedRept;
	$rept =~ m/
	(?<head> [\S\s]* ===\sSummary\s===) \n+

	Total \s read \s pairs \s processed \: \s+
	(?<totalReadPairs>[\d,]+) \n \s+
	#' legendGen
	#' A function to generate colour legends
	#' @param z.range a numeric vector of length 2
	#' @param col a list with elements names low, mid and high with character vectors of length 1 containing colour names DEFAULT \code{list(low = 'lightgrey', mid = 'purple', high='green')}
	#' @param nbins the number of bins in which to split the colours DEFAULT 20
	#' @param nticks the number of axis ticks to display on the legend DEFAULT 5, setting to NA yeild just high and low tags
	#' @param smooth boolean should the colour gadient be interpolated or left discrete? DEFAULT FALSE
	#' @param title the title of the legend
	#' @param tickFormatFunc a function to format the axis ticks e.g \code{function(x) {sprintf("%.e",x)}}
	#' @param draw draw the function directly or return a grob for use in larger plots DEFAULT TRUE
	# NB setwd to meffil/data-raw
	library(devtools)
	library(meffil)
	library(minfi)
	library(FlowSorted.CordTissueAndBlood.EPIC)

	assign("reference.globals", new.env(), envir=environment())

	load.env <- function(filename, env) {
	if (file.exists(filename))
	########################################################################################################################
	## createAnnotationPackage.rn6.R
	## created: 2019-02-04
	## creator: Richard J. Acton
	## ---------------------------------------------------------------------------------------------------------------------
	## Annotation package creation for rn6.
	########################################################################################################################

	## F U N C T I O N S ###################################################################################################
	# Libs
	library(UpSetR)
	library(jsonlite)

	# Functions

	# from: https://github.com/hms-dbmi/UpSetR/issues/85#issuecomment-327900647
	fromListNamed <- function (input) {
	# Same as original fromList()...
	elements <- unique(unlist(input))