Customize Plot Axes

To customize the plot axes, open the inspector window (using the Plot Inspector menu command or tool bar icon) and click on X Axis or Y Axis tabs. Alternatively, you can double click on the x or y axis labels region in the plot to open it in the inspector, or single click if the inspector is already open. The options are:

Automatic - check this box to have PublishPlot calculate axis tick marks for you. Uncheck it to manually select tick mark settings.
Minimum, Maximum, Interval, and Minor Ticks - When automatic is not checked, you can manually enter values for where to start and end tick labels, the interval between labels, and the number of minor tick marks between major tick marks with labels. The maximum number of labels is 50.
Major tick marks are always at multiples of the tick interval setting and minimum and maximum need not be at a tick mark. Log axes usually set the interval to 1 (meaning one decade per interval).
Log Axis - check to make a log axis. When automatic is unchecked, enter actual numbers for minimum and maximum (not log of the number), the interval must be an integer (and it is decades per label) and any non-zero minor ticks will draw log minor ticks between all decades (the actual number does not matter; any non-zero value will give 8 minor tick marks and zero will omit those marks).
Include Zero - When automatic is checked, this box can be selected to force 0 to appear along that axis even if the data does not include zero.
Ticks Inside and Ticks Outside - Check one, both, or neither to have tick marks inside and/or outside the plot. Each plot maintains separate settings for plots framed in a box or plot using axes. The active settings correspond to the current plot style.
Axis Title - You can double click either axis title to enter new text in place (when done type return, tab, or enter). Alternatively you can change the title text in the plot inspector. Click the font or color icons in the inspector to set the font or color for the label. Note that font sizes are always scaled. The point size you select will be the point size when the plot is a full-page, landscape-mode plot. High quality plots should usually have text that is 18 points or larger.
Tick Labels - Click the font or color icon to set the font or color for the major tick mark labels.

Note: Axis titles can have subscripts and superscripts.

Note: You can set the color of axis titles or tick mark labels by dragging a color from any color window on top the that text. You can set opacity of the colors in the color panel.

Note: You can drag a single line text from another application on top of an axis title and that text will become the title for that axis.

Customize Frame

To customize the plot frame, click on the Frame tab in the inspector window. Alternatively, you can double click in the plot frame (but away from any plotted data set or annotation) to open it in the inspector, or single click if the inspector is already open. The options are:

Style - select frame to draw box around the plot or axes to draw x-y axes through the origin entered in the two fields.
X:, Y:, and Labels on Axes - When you select axes through the origin, you can enter the coordinates of the origin and the location of major tick mark labels. Checking labels on axes will place the labels along the axes. When it is unchecked, the labels are outside the plot area.
Recolor Plot - recolor the plot using the color scheme selected in the "As:" popup menu below the button. To recolor a plot, choose a color scheme and then click the button. See below for details on recoloring plots.
Background Color - change the background color for the plot. Use the "Opacity" field to set opacity for the background color in the range of 100% (completely opaque) to 0% (completely transparent. If you drag a plot to other software (e.g., PowerPoint or KeyNote), you can use opacity to let some or all of the background in the other software show through (e.g., a gradient color scheme in PowerPoint or KeyNote).
Separate Edge Color - when checked, the above background color will be background of the plot area while the settings for an edge color will be the background color for all areas outside the plot. Use the "Opacity" field to set separate opacity for the edge color (as explained for background color above).
Line stroke - set width of lines for the box or the axes and for major tick marks. Minor ticks, when drawn, are slightly thinner. Line width is set as a percentage of the plot diagonal (0.14% is about 1 pixel on a full-page, landscape-mode plot). The color box sets the color of the frame or axes (the color well after "Tick length" sets color for tick marks).
Tick length - sets length of major tick marks as percentage of the plot diagonal. Usually ticks are longer than 1%. Minor ticks, when drawn, are slightly shorter. The color box sets the color to use for drawing tick marks.
Major ticks form grid - when checked, major tick marks will extend across the entire plot forming a grid.
Minor ticks form grid - when checked, minor tick marks will extend across the entire plot forming a grid.
Pattern Spacing - sets the distance between lines in patterns as percentage of the plot diagonal. This setting applies when symbols are filled with a pattern.

Note: You can set the frame color by dragging a color from any color window on top of the plot area (and away from any plot data or annotation). To set the background color, however, you have to use the color button in the Frame tab. Fill colors have a field to set opacity, but you can set opacity of any color in the color panel.

Recoloring Plots: Many scientific journals impose extra costs to publish color plots. To avoid such costs, you can recolor a plot by picking and an option from the pop-up menu and then clicking the "Recolor Plot" button. The recoloring options in the pop-up menu are:

B&W - convert all plot features to be either black or white. Plots with more than one data set will need labels, symbols, or line styles to distinguish them.
Gray Scale - convert all plot features to gray scale based on intensity of any colors currently in use. Most (maybe all) journals will print gray scale plots without extra charge.
Viridis, Magna, Inferno, Plasma - convert to a perceptually uniform color scheme. These color schemes are designed to get near linear increase in "perceived lightness" as well as monotonic increase based on color intensity. Their advantage when publishing plots is that they can be printed in B&W (using gray scales) and convey the same information as when printed in color. Many journals only charge for printing color figures while on-line versions can use color. You can submit one plot with these color schemes and it will look good in gray scale printing while appearing in color when on-line.

The best way to create plots with perceptually uniform color schemes is to create the plot first using gray scales and then when done, convert to a perpetually uniform color scheme. For example, imagine a plot with a series of curves for experiments at different temperatures. Create the plot, set curves to gray scale values related to temperature, and finally convert to a perceptually uniform scale (Inferno is a good one to represent temperatures).

Note that perceptually uniform color schemes do not cover the enter range of intensities. For gray scale intensity from 0 to 100%, Viridis goes from 20.0 to 68.1, Magna goes from 0.5 to 90.9, Inferno goes from 0.5 to 87.7 and Plasma goes from 20.3 to 68.2. When you convert colors outside these intensities, they will be mapped to within this range. Two exceptions are pure white (100% intensity) or pure black (0% intensity). These colors, commonly used for labels and plot boarders, will be left unchanged.