aaronwolen

#!/bin/bash

# Partially convert Rnw presentations to Rmd syntax
# - [x]: Code chunks
# - [x]: Section headers
# - [x]: Slide headers
# - [x]: Presenter notes
# - [x]: Lists
# - [ ]: Inlinde code (sort of, not really)

aaronwolen

```{r}
library(microbenchmark)

set.seed(1024)
nr <- 1e4
nc <- 100

m <- matrix(runif(nr * nc), nrow = nr, 
            dimnames = list(paste0("g", seq_len(nr)),
                            paste0("s", seq_len(nc))))

aaronwolen

library(microbenchmark)

set.seed(1024) nr <- 1e4 nc <- 100

m <- matrix(runif(nr * nc), nrow = nr, dimnames = list(paste0("g", seq_len(nr)), paste0("s", seq_len(nc))))

aaronwolen

 ##############################################################################
 #                        Calendar Heatmap                                    #
 #                                by                                          #
 #                         Paul Bleicher                                      #
 # an R version of a graphic from:                                            #
 # http://stat-computing.org/dataexpo/2009/posters/wicklin-allison.pdf        #
 #  requires lattice, chron, grid packages                                    #
 ############################################################################## 

## calendarHeat: An R function to display time-series data as a calendar heatmap 

aaronwolen

# A few simple rules from Stephen Wolfram's A New Kind of Science

apply_rule <- function(x, rule = "254") {
  stopifnot(length(x) == 3)
  stopifnot(all(x %in% c(0, 1)))
  
  rules <- list("254" = c(1, 1, 1, 1, 1, 1, 1, 0),
                "250" = c(1, 1, 1, 1, 1, 0, 1, 0),
                "90"  = c(0, 1, 0, 1, 1, 0, 1, 0),
                "30"  = c(0, 0, 0, 1, 1, 1, 1, 0))

aaronwolen

(* 
	display-specific fullscreen behavior
	
	enable fullscreen for specific applications on MacBook and disable fullscreen
	when using a larger external display

	adapted from:
	* https://gist.github.com/dsummersl/4175461
	* http://daringfireball.net/2006/12/display_size_applescript_the_lazy_way
*)

aaronwolen

#' Extract labels and values from phenoData characteristics columns
#'
#' @details
#' characteristics_ch1.1 characteristics_ch1.2       age  batch
#'                age:54               batch:1  -->   54      1
#'                age:35               batch:2        35      2

parse_characteristics <- function(x, sep = ": ") {
  
  

aaronwolen

---
title: "test"
output:
  html_document:
    keep_md: yes
---

```{r}
library(qtl)
library(qtlcharts)

aaronwolen

# Identify clusters of contiguous factors within a dendrogram
# Aaron Wolen
#
# See http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038422
# for an example situation in which this would be useful
#
# x: dendrogram
# f: a named vector containing the factor that defines the grouping of leaves,
#    must be named using the same values that define x's leaf labels

aaronwolen

# Extract and append multiple values embedded in rows
#
# data: data.frame
# col: column name containing embedded values
# sep: regular expression to split column by
#
# df <- data.frame(key = c("a", "a;b", "a;b;c"), val = 1:3)
# unembed(df, "key", ";")

unembed <- function(data, col, sep, ...) {