.Rprofile

# Template for ~/.Rprofile script

# environmental variables:
Sys.setenv(
	AUTHOR="Conrad Stack",
	EMAIL="conrad.stack@someserver.com"
)

# options():
options("stringsAsFactors"=FALSE)
options(max.print=1000)
options(scipen=1)

# Turn on tab-completion for packages
utils::rc.settings(ipck=TRUE)

# Change default behavior of q() to not save
q <- function (save="no", ...) {
  quit(save=save, ...)
}

## Create a new invisible environment for all the functions to go in so it doesn't clutter your workspace.
.env <- new.env()

## Read data on clipboard.
.env$read.cb <- function(...) {
	ismac <- Sys.info()[1]=="Darwin"
	if (!ismac) read.table(file="clipboard", ...)
	else read.table(pipe("pbpaste"), ...)
}

## Strip row names from a data frame (stolen from plyr)
.env$unrowname <- function(x) {
    rownames(x) <- NULL
x
}

## Open Finder to the current directory on mac
.env$macopen <- function(...) if(Sys.info()[1]=="Darwin") system("open .")
.env$o       <- function(...) if(Sys.info()[1]=="Darwin") system("open .")

## Show the first 5 rows and first 5 columns of a data frame or matrix
.env$hh <- function(d,n=5) if(class(d)=="matrix"|class(d)=="data.frame") d[1:n,1:n]

## Return the number of unique elements in x
.env$n.unique <- function(x){
	length(unique(x))	
} 

## Return the indices of the top n elements from numeric vector, vect
.env$which.high <- function(vect, n=5){
	thresh = min(head(sort(vect,decreasing=TRUE),n))
	which(vect >= thresh)
}

## Return the indices of the bottom n elements from numeric vector, vect
.env$which.low <- function(vect, n=5){
	thresh = min(head(sort(vect,decreasing=TRUE),n))
	which(vect >= thresh)
}

## Return the indices of the elements containing NA
.env$which.na <- function(vect) which(is.na(vect))

## Load cacao genome packages
.env$load.genomes <- function(.criollo=FALSE){
	library("BSgenome.Tcacao.MarsInc.v11")
	library("TxDb.Tcacao.Geneious.pub3i")
	if(.criollo) library("BSgenome.Tcacao.CIRAD.v10")
}


## Attach all the variables above
attach(.env)

(TODO) Need to come up with an easy way to install these on windows machines