The Daily Dongle

working on tab delimited text files -> flowjo

One of the very first posts on the DD, and one of the most frequent - and oldest- of feature requests, is to read in non-flow files into FlowJo. Currently the mac version sort of does this, but you have to hand-write the text header. 

I think we can improve that by just supporting any (for starters, tab delim'd data) 2D array text file and figure out the ranges on the fly. And even make an FCS file out of it. I hope to have a demoable prototype before CDW. For now I'm limiting my scope to 10bit FCS2 format (bigger/smaller data will be normalized to "fit" in ten bits).

BD's multicolor flow utils

http://www.bdbiosciences.com/research/multicolor/tools/index.jsp

neat!

FlowJo translation project

We're starting to translate FlowJo into other languages. Please leave a comment on this post if your language should be added to the list. Currently we are making progress in Chinese and Polish (we just happen to have prolific translators fluent in these, as well as German and French, which will likely be next.)

 Anything else?  

We might be interested in translators for languages other than the four mentioned - unicode experience is a must. Let us know if you'd be into it, and maybe we can discuss how to make it worth your while (probably limited to feel-good-points and T shirts.) FlowJo pratar inte Svenska!

7.5 beta - 3D overlays, with transparency

quicktime tutorial, ~1.5MB: click on the graphic below to download the movie explaining how it works.

Text version: 

- edit prefs file, include "offset3D="1" somewhere in the <prefs... > element. 

- restart FJ

- open a graph window, format Y axis as histogram

- drag that node to the layout

- drag other gates on top of the first plot

- right-click, offset histograms

- use the handle on the lower-right edge of the plot to adjust perspective. 

- use the legend (right-click) to set coloring, line weight, style etc.. as usual. 

visualizing apache server stats in FlowJo

Using the old FJTEXTDATA trick, I loaded some HTTP stats into FlowJo and viewed it as listmode data. First, I chose to correlate Days of Week and Months of Year vs. Hits. I extracted Days of Week by doing a number series (1-7 repeated ). I did the same trick for months assigning them values of 1-12. FInally each event was tagged with that day's hits. So one event on this scale is one day, and the values of that event are {hits, day of week(1-7) and month of year (1-12). Enough words. Pictures: 

Sundays got labeled as 8 for some reason, otherwise looks as predicted. 

Gated for Saturday and Sunday events only, here's a kinetics platform view (each timeslice is ~1 year) 

vs weekday stats..

and even in 3D: 

hacking polyvariate platform for precise controls

If you've ever used the polyvariate platform, you might have noticed the only way to control it is with your mouse, which is imprecise.

if you would like full hands-on control of the PV platform, save your FJ workspace as XML (file/save as xml) and look for these snippets:

<VectorTransformation VectorPivot="0.25" XMin="0" XMax ="1" YMin="-1" YMax="0">
<VectorDefinition Parameter="FSC-A" Pivot="0" XFactor="1" YFactor="0" />
<VectorDefinition Parameter="SSC-A" Pivot="1" XFactor="0" YFactor="1" />
<VectorDefinition Parameter="&lt;FITC-A&gt;" Pivot="0.25" XFactor="0" YFactor="-1" />
<VectorDefinition Parameter="APC-W" Pivot="0.25" XFactor="-1" YFactor="0" />
</VectorTransformation>

the top level element variables are the radius of the circle (out of 1 max), and positions of the X and Y axis sliders.

all of the subsequent elements show three variables: the pivot point, and the magnitude of the radial vector expressed in X and Y components: (1,0) is 3 o'clock, (0,0) is the origin, (-1, -1) is a median between 6 and 9 o'clock

You can change the values for each attribute, save your .xml, rename it to .xml.jo and re-open in FJ.

Three Dee

27MB quicktime demo of the 3D platform. Click pic below to access the link. The work on 3D data display is credited to Francis Bull and Dominic Blais, utilizing JMonkey Engine.

FlowJo learns new command line arguments

FlowJo has finally learned two critical command line tricks: -quit and -save (Thanks Jay!)

Usage:

FlowJo.exe templateFile.wspt folderWithFcsFiles -save -quit

you can enter this command into a .bat file and add a Windows Task so it gets executed every so often (for instance, when new files are deposited into 'folderWithFcsFiles').

the '-save' switch will create a workspace document with the result of the template.

the '-quit' switch will close the program when all calcs are done and all outputs are saved.

This can be coupled with other features of templates, such as autobatching, to create full reports along with outputs which can be routed to PDF, PPT or other files.

I'm making an example walkthru soon, to be posted here as a tutorial.

posted 7.5 beta 96, introduces layout calculations

http://umpqua.treestar.com/bin/FlowJo_7.5.exe

This update fixes:

3D plots teaser

quicktime, 14MB demo - clicky here

I'm working with Mr. Dominic Blais to bring JMonkeyEngine swiftness into the long sought-after 3D display platform for flow. I can't share the application with you as it's too raw, but here's an early peak at current performance on a 20,000 event DIVA file.