Instructions for Creating a Color Scale

This document is also available for download pdf or word format.

Introduction

The color scale is one of the final touches to the figure.  It provides the reader with the scale for evaluating what the colors represent in terms of numerical values.  This scale is easy to create and provides great value to the figure.

Procedure

The steps for making a color scale are exactly the same as processing the data in excel for doing a SAM analysis, generating a cluster, and compiling a heatmap.  The difference is that only one sheet is required and it’s simple to make (see figure below).

The numbers in the ID column correspond to a range of raw intensity values.  The numbers in the Scale column correspond to the processed values.  For example:

Note that I used the value of 10 for the last entry since we assign all values <10 equal to 10.

Save the file in both excel and text format.

Make a Heatmap of the color scale (see instructions for generating a Heatmap in the Howto Use Cluster and Howto Use TreeView documents).  Note that you should use the same contrast and pixel size as the image the color scale corresponds to.

The file product of the Cluster and TreeView procedures should be a *.ps file.

Starting from a *.ps file that is ready for Illustrator

Launch Adobe Illustrator

Select File, Open (Ctrl-O) and choose the color_scale.ps file for the figure

One should see an image like the one shown below (image uses a contrast setting of 5.5)

Left click anywhere on the image to highlight everything

Select Type, Font, Times New Roman, Bold^[1]

Select Type, Size, 10 pt^[2]

Right click anywhere on the highlighted image and select Ungroup

Left click anywhere off the highlighted image to de-select (un-highlight) it

Drag the mouse around the word Scale and delete it

Drag the mouse around the complete color scale

Right click anywhere on the highlighted image and select Group

                Note that here one could save the color scale as an Adobe Illustrator file for use in multiple figures

With the entire image still highlighted, select Edit, Copy (Ctrl-C)

Open the figure that this color scale will go with (see Howto Create a Figure.doc for figure instructions)

Select Edit, Paste (Ctrl-V)

Move the color scale to the best location near the figure

Save the figure with its color scale as an Adobe Illustrator file

1] This font is only a suggestion.  Other fonts may be more appropriate for the figure and will depend on the journal or personal preference.  I've found that Arial Narrow, Bold works well too! It’s important to match the font (type and size) to the figure.

[2] This size is only a suggestion.  Other sizes may be more appropriate for the figure and will depend on the journal or personal preference.

Brian A. Kidd Ó 2004