The Daily Dongle

Orderly Export of Tables from FlowJo PC to Excel

Export a table from FlowJo 7.x into Excel  with the following fun steps:

1. Drag populations and statistics into Table Editor.


2. Click the Batch button and open the Excel tab.
   
   
3. Click the drop-down menu and select Excel.      (CSV will work too)


4. Choose a file name and destination. Check Open file after creation.


5. If Excel is set to open .xls (and CSV)  files on your computer, the file will open in Excel.

You can also export to Excel after making the table inside FlowJo. (Batch button, then the FlowJo tab)
From the top of the FlowJo table, select  FILE > Save as... > Excel

- Don Gull

To save graphics from the layout editor for use in Photoshop:

Go to FlowJo > Preferences...
On the Output tab select the file format you want from the drop-down menu Save Graphics as: Photoshop will accept BMP, JPEG, PHOTOSHOP, PNG
In the layout editor put the desired graphics by themselves in a layout.
Click the floppy disk icon in the upper right of the layout editor

 

Save the image to the desktop or some other convenient place.
In Photoshop click File > Place... to open your graphic in Photoshop.

For maximum graphic quality, in the latest version of FlowJo for Mac and PC, an additional format is available called SVG. This format preserves the ability to edit lines, text, fonts and other styles after the graphic leaves FlowJo. Unfortunately, Photoshop will not import this format. Adobe Illustrator and other "vector art" software will open and allow editing of FlowJo graphics.

- Don Gull 

Editing FlowJo graphics in newer versions of Adobe Illustrator

In previous versions/combinations of FlowJo and Illustrator, it was possible to copy, paste and ungroup a graphic from FlowJo in Illustrator. Then you could edit the graphic components using Illustrator's tools.Things have changed but this is still possible.

In recent versions, you must save and "place" in Illustrator rather than copy/paste. Check to see that your output file type preference is set to SVG in FlowJo Preferences:




Then select the desired graphic(s) in the layout editor and click the Save button (it looks like a tiny floppy disk):



In Illustrator, open a document and go to FILE > PLACE

Navigate to the SVG you just saved and click the PLACE button.

Depending on the complexity of the image, you may have to UNGROUP many times. Use the keyboard combination SHIFT + COMMAND + G to ungroup repeatedly.

Now you can edit the individual components of your graphic.

---Don Gull

Getting FlowJo graphics into Powerpoint on a second computer

If you have one shared computer for analysis and another for preparing Powerpoint, here is what you can do to move many plots in your layout to the other computer...

1) You can "batch to printer" and make a pdf of the batch instead of printing
2) You can make the batch in the layout and then print, making a pdf instead of printing.
then...
3) Then you can take the pdf to the other computer and select plots from the pdf for display in the Powerpoint presentation.

To do 1)... Put the samples you will batch in the layout and select "Batch"
In the dialog, select "Direct to Printer" then "Create"

 

This opens the print dialog. If you have already batched into the layout { #2 above} just click the printer icon in the layout.

Select PDF then Save as PDF...

 

Now you will have a PDF with all your plots. Take this to the other computer.
Open the PDF and select the plots you want to show in Powerpoint using the Select tool.

Copy and paste the desired plots into Powerpoint slides.

- Don Gull

Create Translucent Graphs Like FlowJo's Home Page

When you create a Histogram Overlay in FlowJo's Layout Editor, you can display the histograms with a translucent color, rendering the plot easier to read and/or sexier. Histogram transparency is available in FlowJo for PC if you right-click on the sample name in the legend and select Coloring -> Tinted. Other adjustments (like line weight and type) are available from this menu to customize your graphs.

On the Mac, click the little square next to the histogram's color in the legend. (Circled at right.) Select Tinted (with line) from the menu that pops up. If you copy and paste the layout image into PowerPoint, you can:

1. Right-click (control-click) the image and...
2. Select  Ungroup from the menu, then...
3. Double-click an individual histogram and adjust the Transparency slider shown below.

A similar tool is available in Adobe Illustrator. Ungroup, select one histogram then go to the Window-> Transparency tool and use the slider.

- Don Gull -

Instant Movie of Your Data... Easy

You can view a FlowJo graph or layout in movie form. It's quick and easy, it won't hurt the data, and you may be surprised at what you see.

To make a movie, you add an additional parameter to the graph then view the data in relation to 30 or so slices of that parameter. If time is already a parameter in your data it will be the default choice.

But don't get bogged down in mere scientific details. The point here is to just try it once and see if you like the perspective.

• Open a graph and set the axes to forward scatter and side scatter.
• Choose psuedocolor as the graph type and put a check in the Smoothing box.
• From the Graph menu select Make Movie. You will see the dialog below.

• Select a parameter to be your "control."
• Select the Display accumulates..." button to show the data accumulating as more channels of the control parameter are displayed in the movie frames. The Show movie... option is selected by default. You DO have the QuickTime player installed, don't you?
• Click on Make Movie choose a name and directory and wait a moment for the frames of your movie to be created and displayed.

Other graph types make equally interesting movies. You need not choose psuedocolor. The first check box toggles between showing an equal number of the control parameter's channels per frame and and showing an equal number of events per frame. Try both...

You can scrub through the movie by moving the "play head" triangle back and forth along the time line. You can also scrub the movie by clicking or pressing and holding the arrow keys on the keyboard.

You can view the movie I made as I wrote this here.

For all the movie-making details, you can read the Web docs.