Stephen Kelly stevekm

## plotPCAWithSampleNames.R

      
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                igordot
                / plotPCAWithSampleNames.R
            
            
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              January 2, 2016 18:19
            
              
                moved to https://github.com/igordot/genomics/blob/master/functions-r/plotPCAWithSampleNames.R
              
          
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## rubby.md

      
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                stevekm
                / rubby.md
            
            
              Last active
              November 3, 2016 17:09
            
              
                OS X El Capitan installation of Ruby gems for Jekyll setup
              
          
    Setup for GitHub Pages on MacBook with OS X El Capitan
https://help.github.com/articles/setting-up-your-github-pages-site-locally-with-jekyll/
Forget the other junk, use this guid:

http://railsapps.github.io/installrubyonrails-mac.html
works perfectly!
https://help.github.com/articles/creating-pages-with-the-automatic-generator/

  
## dash_button.py
# -*- coding: utf-8 -*-
from time import sleep

import dash
from dash_core_components import Graph
from dash_html_components import H1, Div, Button
from comp import Button
from dash.dependencies import Input, Output, Event, State

app = dash.Dash()

## index.html
<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <title>Title</title>
    <style>
        .box {
            height: 100px;
            width: 100px;
            top: 100px;

## csv2tsv.py
#!/usr/bin/env python
import sys,csv
for row in csv.reader(sys.stdin):
  print "\t".join(row)

## beanplots.R
## reproduce the figures from http://www.jstatsoft.org/v28/c01/paper using ggplot2

library(ggplot2)

## parameters
set.seed(2710)

## Figure 1
d <- rnorm(50)

## beezid_scraper.py
import pycurl
import json
import time
from StringIO import StringIO

i = 0
bnums = []

while True :
	print(str(i))

## volcanoplot.r
# Download the data from github (click the "raw" button, save as a text file called "results.txt").
# https://gist.github.com/stephenturner/806e31fce55a8b7175af
res <- read.table("results.txt", header=TRUE)
head(res)

# Make a basic volcano plot
with(res, plot(log2FoldChange, -log10(pvalue), pch=20, main="Volcano plot", xlim=c(-2.5,2)))

# Add colored points: red if padj<0.05, orange of log2FC>1, green if both)
with(subset(res, padj<.05 ), points(log2FoldChange, -log10(pvalue), pch=20, col="red"))

## python-async-callback.py
"""
We want to run a function asychronously and run a
callback function with multiple parameters when it
returns!

In this example, we are pretending we're analyzing
the names and ages of some people. We want to print
out:

jack 0

## gist:6272854
def line
new File("test.txt").withReader { line = it.readLine() }
println line
	# -- coding: utf-8 --
	from time import sleep

	import dash
	from dash_core_components import Graph
	from dash_html_components import H1, Div, Button
	from comp import Button
	from dash.dependencies import Input, Output, Event, State

	app = dash.Dash()
	<!DOCTYPE html>
	<html lang="en">
	<head>
	<meta charset="UTF-8">
	<title>Title</title>
	<style>
	.box {
	height: 100px;
	width: 100px;
	top: 100px;
	#!/usr/bin/env python
	import sys,csv
	for row in csv.reader(sys.stdin):
	print "\t".join(row)
	## reproduce the figures from http://www.jstatsoft.org/v28/c01/paper using ggplot2

	library(ggplot2)

	## parameters
	set.seed(2710)

	## Figure 1
	d <- rnorm(50)
	import pycurl
	import json
	import time
	from StringIO import StringIO

	i = 0
	bnums = []

	while True :
	print(str(i))
	# Download the data from github (click the "raw" button, save as a text file called "results.txt").
	# https://gist.github.com/stephenturner/806e31fce55a8b7175af
	res <- read.table("results.txt", header=TRUE)
	head(res)

	# Make a basic volcano plot
	with(res, plot(log2FoldChange, -log10(pvalue), pch=20, main="Volcano plot", xlim=c(-2.5,2)))

	# Add colored points: red if padj<0.05, orange of log2FC>1, green if both)
	with(subset(res, padj<.05 ), points(log2FoldChange, -log10(pvalue), pch=20, col="red"))
	"""
	We want to run a function asychronously and run a
	callback function with multiple parameters when it
	returns!

	In this example, we are pretending we're analyzing
	the names and ages of some people. We want to print
	out:

	jack 0
	def line
	new File("test.txt").withReader { line = it.readLine() }
	println line