The Daily Dongle

FlowJo v765 Mac Command Line

FlowJo v7.6.5 has a nifty command line feature extension for templates. (The FlowJo license allows Mac users to run both our C version (currently v9), and our Java version (currently v7.6.5); the feature sets of the 2 programs being slightly different). 

For repetitive analysis workspaces amenable to templates, the command line feature allows one to use a script to run FlowJo, open a template, and have it load/analyze data, and output reports (layouts and tables). Nice to get your computer to do some work while you are at the ballgame, or home asleep!

 

Here is an example:

1. first set up your FlowJo template.

Autobatch templates

(note: currently Layouts and Tables work in templates, group FCS Export won't execute from templates)

2. On your mac use a text editor to write your shell script to open FlowJo with command line arguments.

-Below is a simple example shell script on my mac to open a FlowJo template, load some data (the template outputs a Table, and a Layout), then flowjo quits.

Screengrab before running the script:

(double click image to make larger)

And, after double clicking the file "flowjo765mac autobatch.command"  

(terminal window opens and runs the script, causing flowjo to open, load the template workspace, load data, export a layout and table, and quit)

 

One can use Mac OSX built in Applescript language and/or Automator to make more complex automation scripts, including Folder actions.

OS X Folder Actions guide

FlowJo Table Options

For many FlowJo power users, FlowJo tables are integral to their flow data analysis. A few users have written into support lately asking how to modify the first column of the table (typically sample name).

 

The Issue:

The default in FlowJo tables is to use the same naming convention as the workspace, plus add numbers before the name. People ask how to get rid of the numbers shown in the picture below:

 

Here is how:

In the table editor, before creating the table, one needs to modify the table creation options (iteration). Instead of using the default (Group tubes by numerical order), one can choose to Group by keyword.

With the Table Editor window open, click the Tables Menu and choose Iteration-Options to open the Batch Iteration Options Dialog Window. (pict below). Set the options to Group tubes by keyword $Fil (or sampleID, or whatever keyword you prefer. $Fil is the standard fcs keyword for the original tube filename saved on the cytometer).

 

More info on Table options:

http://www.flowjo.com/v9/html/tables.html

http://flowjo.typepad.com/the_daily_dongle/2011/09/patient-day-tables-keyword-iteration-.html