HOW TO DESIGN SCIENTIFIC GRAPHICS IN ADOBE ILLUSTRATOR
Essential tools and functions
Adobe Illustrator is a powerful vector graphics editing software that has been used by graphic designers for decades. Unfortunately it's not that easy to use, and many functions that you think should be intuitive are not. The reason for that is actually due to the age of the program, and sometimes software updates introduce redundant or byzantine features. Fortunately, it only takes a bit of practice to figure out Illustrator's quirks for the essential functions. No time? Contact me for a quick professional version here: https://illustrator.science/contact
We'll look at some general considerations you'll need to think about when creating a scientific graphic and some tips and tricks. To help put them into context, we'll use this relatively simple modified figure I created for a recent publication:
Cell signaling pathway diagram created in Adobe Illustrator. Figure modified from figure published in Frontiers in Microbiology (2017).
Before you begin
If you are creating a figure for a journal, check the journal guidelines to see if they have specific requirements for figures. Often for graphical abstracts they will give you the dimensions. For example, see the ACS Publications table of contents graphical abstract guidelines here.
Think about whether you want a single-column or double-column figure as this will change the layout of the components in your diagram. Again, check with your journal to see what the dimensions of the columns are.
Setting up your artboard
Most times (unless you are making a graphical abstract or a poster), you want to set up an artboard with the size of printer paper: 8.5" x 11" in the US or A4 elsewhere. Even though your figure is not going to take up the entire page, this will give you an idea of what size to make objects. You can do this by creating a new document (CTRL + N) and entering in the dimensions. For an already existing document, click the artboard tool in the tool panel (or SHIFT + O) and enter the dimensions at the top ribbon or select the presets (use "letter" for 8.5" x 11").
Fonts and sizes
The second size cue that will help you design your figure is the size of font that you use in the labels. Helvetica and Arial and variations are generally the fonts you will want to use. Straying outside of standard fonts will look unprofessional. The neighborhood of font size you should use is 6 pt to 10 pt — anything outside of this range will be too small or too clunky. The font size in the main text used by journals is going to be 9-10 pt; you don't need to go any larger than this.
The example image above uses 8 pt Helvetica, and the rest of the objects (e.g. membrane receptors) are sized appropriately. For comparison, this is the size of the figure when on an A4 sized paper.
Figure in proportion to an 8.5" x 11" paper
Essential tools and functions
Here are some of the essential tools you'll need for designing majority of objects in Adobe Illustrator as it applies to the example image. Some other more involved functions used are distort and transform effects, live paint, and pattern brushes.
Creating shapes and filling with color
Most shapes you'll need to create are rectangles and circles (ellipses). You can find them on the tool panel. To change the color of the shape fill or the shape stroke, look in the tool panel for these icons:
Make sure you've selected the object you want to fill. Double click on the fill or stroke icons to change the colors. For a majority of shapes in scientific graphics, you'll want to keep the border color black. A good stroke thickness to use is 0.5 pt.
Shape fill panel
To fill with gradients, select the object first and go to the gradient button. Make sure the fill is selected in the foreground. You can select either linear or radial gradients. Particularly with the radial option, make sure you don't use too steep of a gradient, which might call too much attention to the actual color of the object.
Gradients can be nice to give some more shape accents to an object that might be round. A second major use of gradients can be to give a sense of motion or depth; for example, the movement into a cell from the membrane to the center of the cell. In the example image, it also leads the eye top to bottom in the direction of the pathways shown.
Applying a gradient fill to objects
Often you will want to create shapes that are not just rectangles or circles. What many people will do is use the pencil tool to freehand draw the shape they want. Sometimes this can work, and perhaps you want more of a "cartoony" look. But in general it will look sloppy. What you can do instead is build up neat looking objects by merging together more precise rectangles and circles. To do this, use the rectangle or ellipse tool to draw objects on top of each other. Then select both objects and go to the pathfinder panel and select the "unite" option.
Drawing arrows
Arrows are very common in scientific graphics for obvious reasons: you need the for biochemical pathways, demonstrating steps in a process, and showing relationships. Fortunately, Adobe Illustrator makes drawing arrows very easy.
First, you have to draw a line with the line or pen tool. Use the pen tool if you want to have curved arrows. To have your line be exactly horizontal or vertical, hold SHIFT while drawing the line. In general, a line stroke (thickness) should be between 0.25 pt and 1 pt. To put an arrowhead on the line, click stroke and find the arrowhead option. The default arrowhead size is typically too big in comparison to the rest of the figure, so you can adjust the size using the scale option below it. Further down the list of arrowhead options, there is also an "inhibition" type arrowhead that is useful in biochemical pathway diagrams.
Also in the stroke options panel you can select "dashed line" to make a dotted line with an arrow.
Settings to put an arrowhead on a line. Note that you can change the size of the arrowhead by changing the percentage below the arrowhead type.
Cropping objects
One of the biggest difficulties people who are new to Adobe Illustrator have is wanting to crop objects. However, there is no cropping tool; the closest function that can accomplish this is with clipping masks.
To make a clipping mask, draw a rectangle around the area where you want to crop. Then select both the objects, right click, and make clipping mask. With clipping masks, no data is actually lost or deleted, which means you can go back and edit the cropped region at any time. To undo, select the clipping mask group, right click, and "release clipping mask." Alternatively, you can double click the clipping mask group, which will allow you to work within the clipping mask and move/edit objects.
Steps needed to "crop" objects using a clipping mask.
Alignment and distribution
Symmetry and alignment along horizontal and vertical lines are very important in scientific graphics because they minimize confusion about the direction that the diagram is flowing and the sequence of events as they occur. In Adobe Illustrator, alignment is fairly simple as long as you are aligning along the vertical or horizontal. Alignment along arbitrary angles or anchor points can be more challenging — CAD software (i.e. AutoCAD) are much better at this.
Let's take a look at the alignment of vertical arrows for example. You can select both arrows at once by holding down SHIFT and going to the alignment panel. The different types of alignment (center, top, bottom, etc) are pretty self explanatory. If you do it this way, the two arrows will align vertically by moving both of their positions. Typically what you will want to do is align with respect to one of the objects. To do that, select both arrows as before and then release the shift key. Then select the object that you want to stay in position while the other object moves. When you do this, the stationary object will have an additional blue highlight to let you know it is a key object. Then align as before.
Aligning two arrows vertically. Note that when you select the upper arrow as a key object, the lower arrow will align in accordance with the upper arrow. This is denoted by the additional blue line that tells you it is selected and a key object. Make sure the alignment settings are set to "align to selection" (see the lower right side of the alignment panel). Once you select a key object, this setting will automatically change to align to key object. If the setting is "align to artboard" instead, the objects will align to the center of the artboard, which is not typically what you will want.
Distributing objects evenly can be accomplished the same way. This was necessary to create the transmembrane regions of the FPR2/ALX receptor shown in the first figure. Adobe Illustrator will allow you to distribute objects evenly across the entire selection area or you can set a specific distance to separate the objects. In order to set a specific distance, you will need to select a key object as seen above.
Both alignment or distribution can be accomplished without these steps with the use of Smart Guides (turn on and off with CTRL + U). Smart Guides is Illustrator's way of guessing what you want to align and snapping objects to others. For example, if you wanted to align the top arrow to the bottom (see image on the right), you could drag it towards the right. The magenta line (shown by the orange arrow) is the software telling you that it will automatically align the two.
Aligning with smart guides
Sometimes Smart Guides prevent you from moving objects where you want because Adobe Illustrator thinks that you want to align one object to another. To prevent this from happening, just shut off Smart Guides with CTRL + U.
Pattern Brushes
The cell membrane as shown in the original figure above was created with a pattern brush. However, a pattern brush is not strictly necessary for the membrane here because it is entirely straight. You could very easily use the alignment and distribution functions as described previously. But if you want a curved cell membrane or want to put it all the way around a circle (cell), you need to create a pattern brush.
The first thing you'll need to do is create a single unit (we'll call it a monomer). We take this monomer and will tell Adobe Illustrator to make polymers out of it. So draw your first phospholipid monomer with the head and two tails. If you group the object (CTRL + G) and copy and paste it, you can use the align function as above to vertically align the two.
Select both groupings and open the brushes drop down panel from the upper tool bar. Click the new brush icon and select "pattern brush" as your option. Note that if you have any color gradients in your monomer, it will not let you create a brush. Either you need to expand the object or remove the gradient before creating a brush.
Creating a pattern brush to make a cell membrane. This is necessary if the membrane has a curve (shown on the right).
There are various options within the pattern brush dialog box that you can test out to get the desired effect. One thing that may be useful is adjusting the spacing between the monomers so that there's a bit of room to see the details of the pattern. The size of the original monomer that you make will determine how big the stroke is initially, but you can always adjust this by changing the stroke width like you would for any line.
Saving and Exporting
The defining feature of Adobe Illustrator is that it is a vector software (to distinguish it from raster). This means that all the lines are just representations of mathematical functions rather than stored pixels. Practically, this means that figures created this way have infinite resolution — you can zoom in or scale the image however you want and there will be no change in resolution. This is only true for your figure IF you keep it as a vector image. However, if you export the image to a .png or .jpg, it will no longer be a vector file.
If you can, keep the image in a vector format when sending it to the journal. The file format that most journals will accept is .EPS and this is a native format to Adobe Illustrator. With this type of file, the journal can create a pdf of your manuscript with the vector image in it, meaning people who read your paper can zoom into the figure without having it pixelate.