02.delete-me.md

This manuscript is a template (aka "rootstock") for Manubot, a tool for writing scholarly manuscripts. Use this template as a starting point for your manuscript.

The rest of this document is a full list of formatting elements/features supported by Manubot. Compare the input (.md files in the /content directory) to the output you see below.

Basic formatting

Bold text

[Semi-bold text]{.semibold}

[Centered text]{.center}

[Right-aligned text]{.right}

Italic text

Combined italics and bold

Strikethrough

1. Ordered list item
2. Ordered list item a. Sub-item b. Sub-item i. Sub-sub-item
3. Ordered list item a. Sub-item

• List item
• List item
• List item

subscript: H2O is a liquid

superscript: 2^10^ is 1024.

unicode superscripts⁰¹²³⁴⁵⁶⁷⁸⁹

unicode subscripts₀₁₂₃₄₅₆₇₈₉

A long paragraph of text. Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

Putting each sentence on its own line has numerous benefits with regard to editing and version control.

Line break without starting a new paragraph by putting
two spaces at end of line.

Document organization

Document section headings:

Heading 1

Heading 2

Heading 3

Heading 4

Heading 5

Heading 6

A heading centered on its own printed page{.center .page_center}

Horizontal rule:

---

Heading 1's are recommended to be reserved for the title of the manuscript.

Heading 2's are recommended for broad sections such as Abstract, Methods, Conclusion, etc.

Heading 3's and Heading 4's are recommended for sub-sections.

Links

Bare URL link: https://manubot.org

Long link with lots of words and stuff and junk and bleep and blah and stuff and other stuff and more stuff yeah

Link with text

Link with hover text

Link by reference

Citations

Citation by DOI [@doi:10.7554/eLife.32822].

Citation by PubMed Central ID [@pmc:PMC6103790].

Citation by PubMed ID [@pubmed:30718888].

Citation by Wikidata ID [@wikidata:Q56458321].

Citation by ISBN [@isbn:9780262517638].

Citation by URL [@{https://greenelab.github.io/meta-review/}].

Citation by alias @deep-review.

Multiple citations can be put inside the same set of brackets [@doi:10.7554/eLife.32822; @deep-review; @isbn:9780262517638]. Manubot plugins provide easier, more convenient visualization of and navigation between citations [@doi:10.1371/journal.pcbi.1007128; @pubmed:30718888; @pmc:PMC6103790; @deep-review].

Citation tags (i.e. aliases) can be defined in their own paragraphs using Markdown's reference link syntax:

Referencing figures, tables, equations

Figure @fig:square-image

Figure @fig:wide-image

Figure @fig:tall-image

Figure @fig:vector-image

Table @tbl:bowling-scores

Equation @eq:regular-equation

Equation @eq:long-equation

Quotes and code

Quoted text

Quoted block of text

Two roads diverged in a wood, and I—
I took the one less traveled by,
And that has made all the difference.

Code in the middle of normal text, aka inline code.

Code block with Python syntax highlighting:

from manubot.cite.doi import expand_short_doi

def test_expand_short_doi():
    doi = expand_short_doi("10/c3bp")
    # a string too long to fit within page:
    assert doi == "10.25313/2524-2695-2018-3-vliyanie-enhansera-copia-i-insulyatora-gypsy-na-sintez-ernk-modifikatsii-hromatina-i-svyazyvanie-insulyatornyh-belkov-vtransfetsirovannyh-geneticheskih-konstruktsiyah"

Code block with no syntax highlighting:

Exporting HTML manuscript
Exporting DOCX manuscript
Exporting PDF manuscript

Figures

{#fig:square-image}

{#fig:wide-image}

{#fig:tall-image height=3in}

{#fig:vector-image height=2.5in .white}

Tables

Bowling Scores	Jane	John	Alice	Bob
Game 1	150	187	210	105
Game 2	98	202	197	102
Game 3	123	180	238	134

Table: A table with a top caption and specified relative column widths. {#tbl:bowling-scores}

	Digits 1-33	Digits 34-66	Digits 67-99	Ref.
pi	3.14159265358979323846264338327950	288419716939937510582097494459230	781640628620899862803482534211706	piday.org
e	2.71828182845904523536028747135266	249775724709369995957496696762772	407663035354759457138217852516642	nasa.gov

Table: A table too wide to fit within page. {#tbl:constant-digits}

	Colors
Size	Text Color	Background Color
big	blue	orange
small	black	white

Table: A table with merged cells using the attributes plugin. {#tbl: merged-cells}

Equations

A LaTeX equation:

$$\int_0^\infty e^{-x^2} dx=\frac{\sqrt{\pi}}{2}$$ {#eq:regular-equation}

An equation too long to fit within page:

$$x = a + b + c + d + e + f + g + h + i + j + k + l + m + n + o + p + q + r + s + t + u + v + w + x + y + z + 1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9$$ {#eq:long-equation}

Special

[WARNING]{.semibold} The following features are only supported and intended for .html and .pdf exports. Journals are not likely to support them, and they may not display correctly when converted to other formats such as .docx.

Link styled as a button{.button}

Adding arbitrary HTML attributes to an element using Pandoc's attribute syntax:

::: {#some_id_1 .some_class style="background: #ad1457; color: white; margin-left: 40px;" title="a paragraph of text" data-color="white" disabled="true"} Manubot Manubot Manubot Manubot Manubot. Manubot Manubot Manubot Manubot. Manubot Manubot Manubot. Manubot Manubot. Manubot. :::

Adding arbitrary HTML attributes to an element with the Manubot attributes plugin (more flexible than Pandoc's method in terms of which elements you can add attributes to):

Manubot Manubot Manubot Manubot Manubot. Manubot Manubot Manubot Manubot. Manubot Manubot Manubot. Manubot Manubot. Manubot.

Available background colors for text, images, code, banners, etc:

white{.white} lightgrey{.lightgrey} grey{.grey} darkgrey{.darkgrey} black{.black} lightred{.lightred} lightyellow{.lightyellow} lightgreen{.lightgreen} lightblue{.lightblue} lightpurple{.lightpurple} red{.red} orange{.orange} yellow{.yellow} green{.green} blue{.blue} purple{.purple}

Using the Font Awesome icon set:

[ Light Grey Banner
useful for general information - manubot.org ]{.banner .lightgrey}

[ Blue Banner
useful for important information - manubot.org ]{.banner .lightblue}

[ Light Red Banner
useful for warnings - manubot.org ]{.banner .lightred}