12/3/2023 0 Comments Facs flowjo graph![]() Leaving this box unchecked will render a pseudocolor density plot with rare events (outliers) excluded (below, left). When smoothing is selected, you have the option “Show Outliers” available. You can smooth a pseudocolor dot plot by expanding the Options menu on the Graph Window and checking the “Smooth” box. Smoothing a pseudocolor plot changes the display to look like a density plot, using color instead of grayscale to indicate population density (see images below). Unsmoothed pseudocolor plots (default) are presented as dot plots where every event is represented by a dot, and it’s color is dependent on how many other events are in its proximity. There are additional options for changing the display of pseudocolor plots smoothing, showing outliers, resolution and dot size. To change the default setting to a different graph type, go to the Preferences menu, select the Graphs button, and under the Graph Type drop down menu select the type of graph you would like. Pseudocolor plots are the default graph type when opening data in the Workspace. In contrast, traditional monochromatic dot plots can be troublesome for teasing out relative population densities (see images below). A smaller fourth population can be seen to the upper left side of the very dense population. In the graph above, 3 distinct populations of cells are immediately discerned, with the densest population in the middle. Blue and green correspond to areas of lower cell density, red and orange are areas of high cell density, and yellow is mid-range (see image below). It is “pseudo” (meaning false) color because the colors used refer to the density of the cells relative to one another, not to the spectra that the cells emit. As the name implies, pseudocolor plots use color to denote areas of high and low population density. That is, they display the relative population density of cell populations within the Graph Window along two parameters. Pseudocolor plots are a type of bivariate density plot. The ever-popular pseudocolor plot is back again in FlowJo v10! Extract more relevant information from your graphical display, get a “feel” for your data, and wow your co-workers with a colorful display of your experimental results.
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