I utilize the system described by Michelle P. Brown in her Guide to Western Historical Scripts from Antiquity to 1600 (Toronto, 1993), but modified for the purposes of presentation on the web. This is especially evident in the case of painted items like the Clopton Chapel. Generally speaking, though:

• Capitals, whether rubricated or illuminated, are given the most prominent color of the glyph proper. They are also set to the line height they appear to have in the text. So, for example, a two-line capital W that is predominantly red will appear thusly:

  Whan that Aprille with his shoures soote.

  The droghte of Marche hath perced to the roote

• Missing capitals will have a blank space provided, mimicking their appearance in the text. The letter will be included in the XML, though, with a @rend attribute of "hidden." Any guide letters will be indicated via note.
• Underlined text will be rendered thusly: text. It will be modfied still further should the underlining be in a different color than the main body of the text. For example, a red underline will appear as follows: text.
• Paraph marks will mimic their color and line height in the text. So, for example, a single-line blue paraph mark will appear thusly:
  ¶
  Heere bigineeth the miller his tale

• Letters touched by rubrication will be rendered thusly: T.
• Expanded abbreviations in the text are indicated thusly: example.
• Damaged but legible material is indicated thusly: example.
• A gap in the text through damage is indicated thusly:......., where the number of dots indicate the likely number of missing letters based on the other witnesses.
• Insertions will be rendered inline with the text as though they were on the same line, and will appear thusly: [insertion]. Any unusual characteristics regarding the insertion will be mentioned via note.
• Deletions will be rendered thusly: deletion
• Substitutions will be rendered inline with the text, and will appear thusly: inertion[insertion]. Any unusual characteristics regarding the substitution will be mentioned via note.
• Specific issues regarding the text will be indicated via a footnote either immediately after the item referenced or at the end of the line. They have been color-coded to indicate the type of note they are:
  • Explanatory notes provide the reasoning for the editorial choices made, with reference to the image provided. They are indicated thusly:¹.
  • Informational notes provide non-editorial contextual information such as particular scribal renderings or relationships between the witnesses. They are indicated thusly:².
  • Notes unrelated either to the specifics of the text or containing both explanatory and informational elements are indicated thusly:³.