"The Looks" - different gaph types in FlowJo

Quick Index:

changing plot types
dotplots
density plots
contour plots
zebra plots
pseudo-color plots
histogram
CDF graph

Changing plot types

The simplest way to change a plot type is by clicking the  icon in any graph. You will get this popup panel:

When  you click on the "graph type" pulldown menu, you will see the following graph types:

Clicking any of the following and selecting "apply" will change your dotplot type. Let's look at each one in detail:

Dot Plots

The only option available with dotplot looks is in the Dot Plots part of "graphs & gates" under Preferences. You can basically control the size and number of dots displayed:

Dotplots are the "legacy" way of looking at different cell populations. It is not the graph of choice if your populations are closely overlapping or if you have a lot (>100,000  events) in your FCS file.
 

Density Plots:

Clearly the monocytes are a lo easier to see with smoothing!

Density plots are recommended for distinguishing clusters of cells in bivariate plots, with scatter or fluorochrome parameters alike. This method makes populations easier to isloate than in Dot Plots in files with high event counts.

Here is a side-by-side demonstration:

Also, the same comparison but with fluorescence graphs:

Contour Plots: http://www.treestar.com/flowjo/v3/html/graphcontours.html

Contour plots are helpful in visually distinguishing populatins which are close together, based on the "slope" of the contours. For the science behind these plots visit the link above.

Here is an example:

In a dot-plot, finding the right quadrant marker placement can prove difficult in populations with poor definitions. Contour and density plots can be used to aid you with visual cues about cell density and probablity everywhere on your bivariate plots. Which quadrant marker location would you choose?

Zebra Plots:

Visually, this plot type is a hybrid of the density plot and the contour plot. It creates high-contrast graphs to distinguish populations from one another. Here is a FCS file with 10^6 events, dotplots vs. zebra:

when compared against the density plot, the CD4-/CD8 dim population is more apparent in the zebra plot:

Pseudo-Color plots:

Basically the color version of a density plot. When smoothed, it really helps to tell those dots apart! Take a look:

The addition of color information on top of the density information introduces better contrast and popluations are much easier to spot! Again, consider the CD4-/CD8 dim cells.

Histograms have their own document, view it by clicking here <link>
 

CDF (or umulative distribution function) have their own document, view it by clicking here.