Skip to content
walkerhound edited this page Oct 8, 2012 · 16 revisions

This wiki is for the Projects repository of Laura Clemens

Table of Contents

Github

github

Wiki

Wiki

Cytoscape

Cytoscape

RedeR

RedeR

R colors

http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.R

http://research.stowers-institute.org/efg/R/Color/Chart/

GetColorHexAndDecimal <- function(color)
{
  c <- col2rgb(color)
  sprintf("%s #%02X%02X%02X   %3d %3d %3d", color, c[1],c[2],c[3], c[1], c[2], c[3])
}

> HexAndDec <- unlist( lapply(colors(), GetColorHexAndDecimal) )

Circos

Circos

GraphViz

http://www.graphviz.org/

Graph Connected Components

Graph Connected Components

Brewer Colors

Brewer Colors

David Gene ID Conversion

David Gene ID Conversion

Update Mouse Genome

Update Mouse Genome

fink

You should now have a working Fink installation in '/sw'. You still need package descriptions if you
want to compile packages yourself. You can get them by running either of the commands: 'fink
selfupdate-rsync', to update via rsync (generally preferred); or 'fink selfupdate-cvs', to update via
CVS (more likely to work through a firewall).

Run '. /sw/bin/init.sh' to set up this terminal session environment to use Fink. To make the software
installed by Fink available in all of your future terminal shells, add '. /sw/bin/init.sh' to the init
script '.profile' or '.bash_profile' in your home directory. The program /sw/bin/pathsetup.sh can help
with this. Enjoy.

Hive Plots

Hive Plots with D3

Complicated Hive Plot

Area Hive Plot

Simple Hive Plot

twitter hive plot

Tricks

Issue with running hiveplots. The error looks like this:

./makehiveplots: ../network/bin/parsedot: /bin/env: bad interpreter: No such file or directory
 /Users/clemensl/projects/hive-plot/linnet-0.02/bin/linnet -conf etc/linnet.conf -file img/hiveplot.lauren.png

xattr -l *
xattr -dr com.apple.quarantine .
http://stackoverflow.com/questions/9952612/mac-os-usr-bin-env-bad-interpreter-operation-not-permitted
sudo ln -s /usr/bin/env /bin/env

https://groups.google.com/forum/?fromgroups=#!topic/circos-data-visualization/JteWKo7zceQ

Clone this wiki locally