Overlays give researchers a powerful way to visualize comparisons between populations.

On a parameter by parameter basis in univariate histograms, by binning two histograms together to reveal a bivariate dot plot, or even applying machine learning to generate derived parameters representing embedded space in a single plot. (such as tSNE and UMAP)


Traditional univariate histograms are a mainstay of researchers in every field. often shown in the style of a “violin” plot for single-cell sequencing, SeqGeq has a variety of customization options for histogram plots (violin plots are currently only available through plugin functionality). Most of the customization options for histogram overlays within SeqGeq’s Layout Editor are available via gestures in the Legends associated with the plot.


Layer Color

To change line coloring, click the colored swatch to the left of any population of interest in the overlay’s legend.

Fill Tint

Many options for histogram customization are available through a right click option on any layer of interest, such as Fill/Tint (aka “Coloring”). Often useful in distinguishing a background and/or control population.

Line Style

Changes to line style can help accentuate different populations used for overlay.

Line Weight

Line weight can also aid in highlight a feature of interest among overlaid populations. In this E.G. a thinner line helps to blend the control population into the background.


Adjustments to smoothing can make plots more aesthetically appealing or better illustrate the modality of populations. Researchers should be careful not to mask populations inadvertently when changing smoothing kernels.


Normalization (aka Y-Axis scaling normalizations) shifts the relative peak heights in an overlay.


Bivariate plots often offer a much more interesting view of phenotypic information.


Increased resolution will aid in the presentation of figures for publication. Note, the dot size for high resolution plots will often require some adjustment.

Dot Shape

Dot shapes can now be adjusted in SeqGeq v1.6 and beyond. Hint: Try holding down the “Alt/Option” key while choosing the dot shape to access additional dot shape options.

Plot Type

Plot types of the background (lowest level) population in an overlay can be adjusted per plot:

Dot Size/Shape Thickness

Both the size and thickness of dots will often make population definition more clear. Particularly useful for highlighting very rare subpopulations in a heterogeneous mix.


For a demonstration of the various overlay illustration options in SeqGeq reach out to schedule a screen-sharing session: seqgeq@bd.com