Dealing with issues of overplotting
Claus O. Wilke
2025-07-05
Be aware of points plotted exactly on top of one another
Technical term for this problem: overplotting
Partial transparency helps highlight overlapping points
A little jitter shows overlaps even more clearly
But don’t jitter too much
2D density plots: Contour lines and contour bands
Contour lines are the 2D version of density plots
Contour lines are the 2D version of density plots
We can vary shading for added effect
What do we do when there are multiple groups?
Colored contour lines can work for 2 to 3 groups
What if there are multiple groups intermingled?
Don’t make plots that look like spaghetti
Contour lines work well with small multiples (facets)
2D histograms: Rectangular and hex bins
2D histograms: rectangular bins
We need to choose a bin size as in regular histograms
2D histograms: rectangular bins
We need to choose a bin size as in regular histograms
2D histograms: hex bins
2D histograms: hex bins
Choosing the right color scale
palette: SunsetDark
Choosing the right color scale
palette: Batlow
Choosing the right color scale
palette: YlOrRd
Choosing the right color scale
palette: BluYl
Choosing the right color scale
palette: Heat
Choosing the right color scale
palette: ag_GrnYl
Choosing the right color scale
palette: SunsetDark
Creating 2D density plots and histograms in R
Contour lines
Getting the data:
# A tibble: 123 × 8
bird_id sex bill_depth_mm bill_width_mm bill_length_mm head_length_mm
<chr> <chr> <dbl> <dbl> <dbl> <dbl>
1 0000-00000 M 8.26 9.21 25.9 56.6
2 1142-05901 M 8.54 8.76 25.0 56.4
3 1142-05905 M 8.39 8.78 26.1 57.3
4 1142-05907 F 7.78 9.3 23.5 53.8
5 1142-05909 M 8.71 9.84 25.5 57.3
6 1142-05911 F 7.28 9.3 22.2 52.2
7 1142-05912 M 8.74 9.28 25.4 57.1
8 1142-05914 M 8.72 9.94 30 60.7
9 1142-05917 F 8.2 9.01 22.8 52.8
10 1142-05920 F 7.67 9.31 24.6 54.9
# ℹ 113 more rows
# ℹ 2 more variables: body_mass_g <dbl>, skull_size_mm <dbl>Contour lines
Contour lines
Contour lines
Contour bands
Contour bands
Contour bands
2D histograms
2D histograms
2D histograms
2D histograms
Hex bins
Hex bins
Hex bins
Further reading
- Fundamentals of Data Visualization: Chapter 18: Handling overlapping points
- ggplot2 reference documentation:
geom_density_2d() - ggplot2 reference documentation:
geom_bin_2d() - ggplot2 reference documentation:
geom_hex()
Dealing with issues of overplotting Claus O. Wilke 2025-07-05