“Visual Hypothesis & Correlation
Discovery for Precision Medicine”
Rumpf, R. W., Gonya, J., and Ray, W. C. 2014. VAHC (submitted).
In order to view the dataset below, please be sure that you have already
downloaded StickWRLD from the
StickWRLD home page. You will have
to have python installed on your computer in order to run StickWRLD. If
you would prefer to have access to a downloadable VirtualBox Virtual Machine
(an Ubuntu instance pre-configured to run StickWRLD) please email the author at
wolfgang.rumpf@nationwidechildrens.org.
You may also find the StickWRLD Manual
of use.
Once you have both StickWRLD and the datasets downloaded, you can use the
"load" command to load the data. As per the StickWRLD Manual:
- Launch StickWRLD (e.g. from the command line type python stickwrld_demo.py (or python-32 stickwrld_demo.py for 32-bit installations of python) while in the
StickWRLD distribution's exec directory)
- From the Data Loader pane, select "Load..."
- Load the data set itself by selecting the desired binning variation
file. You should choose to use no separators in the dialog box.
- Once that's loaded StickWRLD wants you to load the headers file
which contains the column descriptors for the display - select the header file
from the same directory as the binning variation you have chosen.
- The StickWRLD GUI should now load. NOTE: it may take 30 seconds or so on a Core2Duo system,
less on a more modern computer.
If you encounter any errors please be sure you have correctly installed
StickWRLD as per the manual.
Dataset
There are three binning variations of the dataset contained within the zip file
below, each in a separate directory with an appropriate "headers.txt" file for
loading (as above).
FOR BEST RESULTS RIGHT-CLICK ON THE ZIP FILE
AND SELECT "SAVE"
Rumpf-VAHC-data.zip
As described in the paper, this dataset has been encoded into a format which
could be read by StickWRLD. The StickWRLD manual describes the process of
encoding any dataset into the StickWRLD format. If you are planning on
loading biological sequence information (e.g. protein or DNA alignments created
in Clustal), you may convert your Clustal alignment file to StickWRLD format
using this fasta2stick.sh
shell script (requires Mac OS X or linux).
The StickWRLD Data Format/Loading your own Data
For more information on creating custom datasets for use in StickWRLD please
see the StickWRLD Manual.