Plot Appearance

The Customise Plot Appearance options in Add to Plot provide fine-grained control over the visual properties of your plots. These settings go beyond colour, shape, and size to cover transparency, layout, and other visual details.

Transparency (alpha)

Transparency controls how see-through points are. This is especially useful for dense scatter plots where many points overlap:

• Alpha = 1 (default): Fully opaque points
• Alpha closer to 0: More transparent points, allowing overlapping regions to show as darker areas
• When transparency is applied, the point fill automatically changes from transparent to filled, so the alpha effect is visible

Overplotting

If your scatter plot looks like a solid blob, reducing transparency is one of the best ways to reveal density patterns. You can also try jitter or switching to a hexagonal binning plot.

Jitter

Jitter adds a small amount of random noise to point positions. This is useful when data values are rounded or discrete, causing many points to stack on top of each other:

• x: Jitter on the horizontal axis only
• y: Jitter on the vertical axis only
• xy: Jitter on both axes

Jitter does not change the underlying data — it only affects the visual positions of points on the plot.

Rugs

Rugs are small tick marks along the axes that show the marginal distribution of each variable individually:

• x: Show rug marks along the x-axis
• y: Show rug marks along the y-axis
• xy: Show rug marks along both axes

Rugs are helpful for seeing where observations are concentrated along each axis, even when the scatter plot itself is hard to read.

Plot type override

You can override the automatically selected plot type to switch between different visualisations of the same two numeric variables:

• Scatter plot: The standard point-by-point display
• Grid density plot: A grid density representation
• Hexagonal binning plot: A hexagonal binning representation

This is useful if iNZight has automatically selected a large-sample plot type (e.g., hex plot) but you prefer a different view, or vice versa.

Point size

The overall size of points can be scaled up or down using the point size control. This affects all points uniformly (unlike Size by variable, which scales points based on data values).

Point fill

Controls the fill colour of plotted points:

• Transparent (default): Points show only their outline colour
• Fill: Points are filled with their colour, which interacts with the transparency setting

Background colour

Changes the background colour of the plot area. The default is a light grey (#eeeeee). Grid lines automatically adjust their colour based on the background.

Grid lines

Toggle the display of grid lines in the plot area. Grid lines help with reading values but can be turned off for cleaner presentations.

Box plot (dot plots and histograms)

For dot plots and histograms, you can toggle the display of the accompanying box-and-whisker plot, which shows the median, quartiles, and potential outliers.

Applicable plot types

Feature	Scatter	Dot	Histogram	Bar	Hex / Grid
Transparency	✓	✓	—	—	✓
Jitter	✓	—	—	—	—
Rugs	✓	—	—	—	—
Plot type override	✓	—	—	—	✓
Point size	✓	✓	—	—	—
Background colour	✓	✓	✓	✓	✓
Grid lines	✓	✓	✓	✓	✓
Box plot toggle	—	✓	✓	—	—