EditingTips - nsalomonis/altanalyze GitHub Wiki

Tips for Editing this Wiki

In order for the content/appearance of this wiki to be consistent and play nicely with the auto-generated help documentation located on Read The Docs, there are a few suggested guidelines to follow when editing wiki pages here:

Links

Bare URLs (i.e. text copied and pasted from a browser URL bar) end up linking fine on GitHub wiki pages, but just show up as text when moved over to RTD. You need to make them links as follows:

This is a bare URL: http://www.this-page-intentionally-left-blank.org/  
... but this will render properly at RTD: [http://www.this-page-intentionally-left-blank.org/](http://www.this-page-intentionally-left-blank.org/)  
... although better text is better: [Let's get meta!](http://www.this-page-intentionally-left-blank.org/)

This is a bare URL: http://www.this-page-intentionally-left-blank.org/
... but this will render properly at RTD: http://www.this-page-intentionally-left-blank.org/
... although better text is better: Let's get meta!

Lists

To render properly on RTD, lists must have a space before them:

This won't render correctly:
- Point 1
- Point 2

...but this will:

- Point 1
- Point 2

Code Blocks

To get correct rendering and decent syntax highlighting on RTD for blocks of command-line code, javascript (or sometimes bash) seems to work best:

```javascript
python AltAnalyze.py --species Mm --platform RNASeq --filterdir "C:/BEDFiles"
  --altpermutep 1 --altp 1 --altpermute yes --additionalAlgorithm none
  --altmethod linearregres --altscore 2 --removeIntronOnlyJunctions yes
```
python AltAnalyze.py --species Mm --platform RNASeq --filterdir "C:/BEDFiles"
  --altpermutep 1 --altp 1 --altpermute yes --additionalAlgorithm none
  --altmethod linearregres --altscore 2 --removeIntronOnlyJunctions yes

Also, breaking the command up into multiple lines makes it easier to read (no horizontal scrollbar), although admittedly it does interfere with the ability to cut and paste commands.

Figures

A nice way to display figures is to use an h3 header for the figure name (so it can be referenced), followed by a link to the image, a blank line, some text for the caption, then a horizontal rule. The reference name will be the figure name made lowercase with spaces replaced by hyphens and other characters removed (example below):

### Figure: Test
![](images/onlyATest.jpg)

**This is a test:** Had this been an actual figure, it would have been informative. This is only a test.
***

[Show me the figure!](EditingTips#figure-test)

Figure: Test

This is a test: Had this been an actual figure, it would have been informative. This is only a test.


Show me the figure!

Tables

Tables are formatted (and referenced) in much the same way as figures. Simply replace the image link with the table format below (created using pipes |). The table must be preceded by a blank line and there must be at least 3 hyphens in each column of the second row for the table to render properly. You can add whitespace to make the text easier to read (it doesn't matter for the final Markdown display, though):

### Table: Test

| | Column 1 | Column 2 | Column 3 |
| --- |:--- |:---:| ---:|
| Justification | Left | Center | Right |
| Numbers       | 25   | 6      | 2     |

**Data:** Mmmmmmmm, data.
***

Table: Test

Column 1 Column 2 Column 3
Justification Left Center Right
Numbers 25 6 2

Data: Mmmmmmmm, data.


References

A list of reference material for the wiki (papers, etc.) can be found in References. Each citation is formatted as follows, with an anchor name that has the first authors last name and the year of publication:

1. <a name="Doe2016"></a>Doe J, *et al.* (2016) [I can't Google myself!](https://en.wikipedia.org/wiki/John_Doe) *Journal* 1:2-3.
  1. Doe J, et al. (2016) I can't Google myself! Journal 1:2-3.

After adding a new citation there, a pretty link in the text can be made as follows:

You think you have problems?<sup>[\[Doe2016\]](References#Doe2016)</sup>

You think you have problems?[Doe2016]

YouTube Links

While you can't embed a video in a GitHub page, you can add a YouTube link to an image. Using the YouTube video ID in the URL, you can get a thumbnail image of the video from YouTube and display that image with a link to the video like so:

[![](https://img.youtube.com/vi/YOUTUBE_VIDEO_ID/0.jpg)](https://www.youtube.com/watch?v=YOUTUBE_VIDEO_ID)

You've got to see this coming...

Extra HTML Elements

Some extra HTML elements that I know of so far that work fine both on the GitHub wiki pages and on RTD:

  • Anchors:

      [You never take me anywhere!](EditingTips#Lets_go_here)
      
      <a name="Lets_go_here"></a>Here you go.
    

    You never take me anywhere!

    Here you go.

  • Sub/Superscript:

      Been a while since I used L<sup>A</sup>T<sub>E</sub>X.
    

    Been a while since I used LATEX.

  • Links:

      <a href="EditingTips#extra-html-elements">You are here.</a>
    

    You are here.

  • Ordered lists with arbitrary starting numbers:

    Github-flavored Markdown starts lists at 1 by default. If you ever need to break a list up (i.e. have the start of the list, some interrupting text, then the rest of the list), you can use HTML like so:

      1. Item 1
      2. Item 2
      
      May I interrupt for a brief moment...
      
      <ol start="3">
      <li>Item 3</li>
      <li>Item 4</li>
      </ol>
    
    1. Item 1
    2. Item 2

    May I interrupt for a brief moment...

    1. Item 3
    2. Item 4

    NOTE: Any Markdown formatting in the list items may be lost when using HTML ordered lists, so you will have to use the HTML equivalent, like <code>...</code> for inline code or <a href="...">...</a> for links (unfortunately, it appears that relative links like this will not link properly on RTD).

  • HTML image syntax:

    If you need to resize an image, you'll have to use HTML image syntax to do it:

      <img src="images/onlyATest.jpg" width="200"/>
    
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