FlowJo v9 Manual


Generating Publication-Quality Output

FlowJo's sophisticated Layout Editor generates graphics that are publication-ready (or presentation-ready, for slides).� However, you can also easily export the graphics to other programs to use their more complex tools for generating presentation graphics.

After reading the information on this page, you should view some examples of graphs that were easily created in Canvas from plots generated in FlowJo. One example is a contour plot with outliers; the other is an example overlaying histograms.

You can export graphics into other programs in two main ways: (1) simply copy graphs from any graph window and paste them directly into the drawing package; or (2) generate a layout, and either save the output to the clipboard (and paste it directly into a drawing package), or save the output to a disk file and read it from the drawing package. The discussion below applies to both of these export functions.

When you paste a graph into a drawing package (or read it from a disk file saved by a layout), it is a group of objects. You can ungroup the objects and access each one individually. All text is formatted as 12-point Palatino. All lines are one-point wide (with the exception of high-resolution contour plots; see below). The graph of the events themselves (internal to the axes), is either a line-drawing or a bitmap.

All histograms and CDF plots are copied as line drawings. This means that when you ungroup the plot, you can click on the histogram and change its line style (bold, dashed, color) and/or fill pattern (the default fill pattern is "No fill") and color. This allows you to overlay histograms and/or CDF plots easily (simply paste them on top of each other).� (Note that you can also use the Layout Editor to overlay graphics for you).

The other plot styles (contour plots, dot plots, density plots, and pseudo-color plots) are copied as bitmaps by default. A bitmap is a single "paint" object: it does not consist of lines and polygons, but rather of pixels of a particular color. Dot plots and contour plots are "1-bit" bitmaps (black & white); the others are 8-bit depth to allow for color/grey-scale gradations.

Bitmaps have the advantage of being easily and quickly manipulated by drawing programs, and hence this is the default output style. As well, you will find that for most presentations or publications, the bitmap style is adequate. The disadvantage of bitmaps is that they cannot be resized without risking serious distortion problems. This makes the generation of complex figures somewhat more difficult.

Thus, FlowJo gives you the option of setting the default output of these kinds of graphs as draw objects ("high resolution PICT"). This setting is defined in the preferences dialog. When you export graphs as draw objects, then they are easily resized without distortion. In addition, for contour plots, the contour lines are exported as "hairlines", which appear nicer on high-resolution printouts. Because each contour line is a polygon, you have the option to edit the contour lines to be different color or fill patterns to make your plot look exactly how you want.

The drawback of exporting draw objects is that it can be much more difficult for the drawing package to handle. This is especially true for dot plots, density plots and pseudo-color plots! You may find these to take a long time to draw or resize, because each dot (and each "pixel" in the density plots) is actually a separate object. Thus, a dot plot with 10,000 dots has 10,000 objects that the drawing program has to keep track of.

You may want to experiment with different output styles to decide which suits your needs the best.

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