A Scatterplot displays the value of 2 sets of data on 2 dimensions. Each dot represents an observation. The position on the X (horizontal) and Y (vertical) axis represents the values of the 2
variables. It is really useful to study the relationship between both variables. It is common to provide even more information using colors or shapes (to show groups, or a third variable). It is also
possible to map another variable to the size of each dot, what makes a bubble plot. If you have many dots and struggle with overplotting, consider using 2D density plot.
Base R scatterplots
Of course baseR offers a really good option to build a scatterplot as well.
A Manhattan plot is a particular type of scatterplot used in genomics. The X axis displays the position of a genetic variant on the genome. Each chromosome is usually represented using a different color. The Y axis shows p-value of the association test with a phenotypic trait.