kcha

# Create a color bar and breaks that center at a specific value
# Source: https://stackoverflow.com/a/10986203
colorbar <- function(min, max, threshold=0, palette="RdBu", palette_length=15) {
    pal <- rev(brewer.pal(9, palette))
    
    # Get all possible breaks
    my_breaks <- seq(min, max, length.out=palette_length)

    # Get number of breaks above threshold and below threshold
    above <- length(which(my_breaks > threshold))

kcha

#!/bin/bash
#
# Backup R Markdown authored HTML files to a "notebook" sub-directory and add
# a timestamp to the HTML file
#
# e.g.
# R_analysis.html -> notebook/R_analysis.2015-02-12.html
#
# If file is version controlled, then a short commit hash is also added.

kcha

#!/usr/bin/env python

from __future__ import print_function
from six import iteritems
import sys
import os
import os.path
import re
import argparse
import pandas as pd

kcha

# Split a data frame into k subsets
#
# Returns a list of subsetted data frames of equal (or as close to equal as 
# possible) size. If the data frame cannot be split equally by k, then the
# remainder will be adding to the last k'th subset. User can also request
# to put the remainder in an additional k+1 subset.
#
# This is basically a wrapper around split(), but helps calculate the remainder,
# if necessary.
split_k <- function(x, k, remainder_as_additional = FALSE) {

kcha

# Source: http://stackoverflow.com/a/9314880
color.bar <- function(lut, min, max=-min, nticks=11, ticks=seq(min, max, len=nticks), title='') {
  scale = (length(lut))/(max-min)
  # dev.new(width=1.75, height=5)
  plot(c(0,10), c(min,max), type='n', bty='n', xaxt='n', xlab='', yaxt='n', ylab='', main=title)
  axis(2, round(ticks, 2), las=1)
  for (i in 1:(length(lut))) {
    y = (i-1)/scale + min
    rect(0,y,10,y+1/scale, col=lut[i], border=NA)
  }

kcha

library(readr)
library(dplyr)
library(tm)
library(wordcloud)
library(SnowballC)
library(RColorBrewer)

m <- read_csv("node_table.csv.gz") %>% 
  filter(EM1_fwer_qvalue_dataset1 < 0.5, EM1_gs_size_dataset1 > 95) 

kcha

N=4     # Chunk size
C=0     # Counter

for i in {1..12};
do
    # submitjob here...
    echo $i
  
    ((C=C+1))
    if [[ `expr $C % $N` == 0 ]]; then

kcha

#!/bin/bash
 
check_exit_status() {
    # Checks the latest exit status and exits if status is non-zero
    # usage: check_exit_status $? "my_function"
    EXITSTAT=$1
    FUNC=$2
    if [ "$EXITSTAT" -ne "0" ]; then
        echo "=> ["`date`"] $FUNC failed"
        exit $EXITSTAT

kcha

# these examples rely on the R/qtl package, www.rqtl.org
# install R/qtl package, within R, by typing install.packages("qtl")

all: knitr_example.html knitr_example_asciidoc.html knitr_example.pdf markdown_example.html

R_OPTS=--no-save --no-restore --no-init-file --no-site-file # vanilla, but with --environ

knitr_example.html: knitr_example.Rmd
	R ${R_OPTS} -e 'library(knitr);knit2html("knitr_example.Rmd")'

kcha

#install if necessary
source("http://bioconductor.org/biocLite.R")
biocLite("seqLogo")
biocLite("Biostrings")

library(seqLogo)
library(Biostrings)

strings <- c("GATTACA", "GATAACA", "GATAAAA", "GATTAGA")