View source for User:Was a bee/Gene

<div align="center">
	<div style="position: relative; width: 300px;">[[File:Human chromosome 7 ideogram.svg|300px|Human chromosome 7]]
		<div style="position: absolute; left: 194px; top: 1px; padding: 0;">[[File:HSR 1996 II 3.5e.svg|14px|Genomic location for AAA gene]]</div>
		<div style="position: absolute; left: 200px; top: 18px; padding: 0;">[[File:Red rectangle 2x18.png|2px|Genomic location for AAA gene]]</div>
	</div>
</div>
[[File:HSR 1996 II 3.5e.svg|15px]]
[[File:Red triangle.svg|15px]]
[[File:Emoji u1f53b.svg|14px]]
[[File:Bild 30 - Vorfahrt auf der Hauptstraße achten! StVO 1937.svg|15px]]
[[File:Red triangle penal.svg|15px]]
[[File:Red Arrow Down.svg|15px]]
[[File:Red arrow downwards.jpg|15px]]
[[File:Hjärta.gif|15px]]
[[File:HSR 1996 II 3.5f.svg|15px]]
[[File:HSR 1996 II 3.5g.svg|15px]]
[[File:Twemoji 25c0.svg|15px]]
[[File:Twemoji 25b6.svg|15px]]

== 1. Test ==
A test trying to put a marker icon automatically onto the chromosome ideogram image to show location of gene (based on basepair position data stored in wikidata).

In other words, trying to make the image like below automatically.

[[File:SHH location.png|300px|thumb|left|Location of [[Sonic hedgehog|Sonic hedgehog gene]]]]

Currently in Wikimedia Commons, there are about 100 ideogram images which are used to show gene position. See [[:commons:category:Human chromosome ideograms which indicates gene location]].

[[File:Red rectangle 4x18.png|thumb|left|4px|This is marker icon]]

[[File:Human chromosome 7 ideogram.svg|thumb|left|300px|This is plain ideogram of chromosome 7. Whole ideogram set is here [[:commons:Template:Human chromosome ideograms in svg]].]]

{{-}}

==2. Result ==
{|class="wikitable floatright" width="325px"
|+ Test result
|-
|colspan="2" |
<div align="center">
{{Superimpose2
  | base = Human chromosome 7 ideogram.svg
  | base_width = 300px
  | base_link = File:Human chromosome 7 ideogram.svg
  | float = Red rectangle 2x18.png
  | float_width = 2px
  | float_alt = an arrow
  | float_caption = 
  | link = File:Red rectangle 4x18.png
  | t = 
  | x = 288.2
  | y = 17
}}
</div>
|-
|Bp start || 155,799,986 
|-
|Bp end || 155,812,273
|-
|}
Good (see the test case box at the right)
<!--
You could possibly noticed that band patterns and arrow position of the top image and of the right look differ slightly (although it is difficult to detect).

But both images and arrow positions are correct. This is because...

The top ideogram shows band patterns what you can see under microscope. Standard images for this kind of idiograms are published by [[ISCN]] (International System for Human Cytogenetic Nomenclature). For example, see [http://atlasgeneticsoncology.org/ISCN09/Chrom7ISCN09.html this website]. In this type of idiograms, some regions are more condensed (have more basepairs), some other regions are more sparse (have less basepairs).

On the contrary, the ideogram image at the right is drawn proportional to basepair length. As far as I know, all major genetic databases ([[genome browser]]s) use this format. 
-->

{{-}}

==3. Calculation detail ==
The position where the marker should be put is calculated as follows. Although math expression looks something complex, actual calculation is not so complex. The concepts which are used here are basically only plus and minus for calculating [[length]], and multiplication and division for calculating [[Image scaling|scaling]].
{{hidden|
| style = border:1px dashed red; width: 90%;
| headerstyle = background: #ccccff; font-size: 110
| header = Calculation detail
| content = Other concepts used here are... Dividing sum of gene-start and gene-end by 2 is to get mid point of the gene. Dividing arrow-width by 2 is because image position is set by leftist point of the image, not by the center of the image. Conditional branch for arrow-width is just a technical problem which is needed to choose different shape of rectangles among these ([[:commons:Template:Red rectangle series]]) as a marker depending on target gene length.




Calculation algorithm is as follows....
<math>PositionSetX = \Bigg\{ pterPx + \bigg[(qterPx - pterPx) \times \frac{\frac{({\color{Red}GeneStart} + {\color{Red}GeneEnd})}{2}}{{\color{Red}ChromosomeLength(n)}} \bigg] \Bigg\}  \times \frac{ImageShownWidth}{ImageOriginalWidth} - \frac{{\color{Blue}ArrowWidth}}{2}</math>

<math>{\color{Blue}ArrowWidth^*} =(qterPx - pterPx) \times \frac{({\color{Red}GeneEnd} - {\color{Red}GeneStart})}{{\color{Red}ChromosomeLength(n)}} \times \frac{ImageShownWidth}{ImageOriginalWidth}</math>

<math>{\color{Blue}ArrowWidth}=\begin{cases}2 & \ ({\color{Blue}ArrowWidth^*} < 2) \\ \lceil {\color{Blue}ArrowWidth^*} \rceil & \ (otherwise. \lceil\; \rceil \; is \; ceiling \; function) \end{cases}</math>

[[File:Gene Infobox Location Math.png|thumb|left|800px|Math in one picture]]
{{-}}
Where {{Font color|red|'''''red terms'''''}} are variables retrieved from Wikidata, the {{Font color|blue|'''''blue term'''''}} is the term calculated based on variables retrieved from Wikidata, and other '''''black terms''''' are constants. 
* <math>{\color{Red}GeneStart}</math>: Gene start position from the terminus of p-arm. (unit: basepair, example: 155799986 from [[:wikidata:Q14860072]])
* <math>{\color{Red}GeneEnd}</math>: Gene end position from the terminus of p-arm. (unit: basepair, example: 155812273 from [[:wikidata:Q14860072]])
* <math>{\color{Red}ChromosomeLength(n)}</math>: Length of the <math>n</math> th chromosome which contains the target gene. (unit: basepair, example: 159345973 for [https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh38.p10 chromosome 7])
* <math>pterPx</math>: Horizontal position of pter (tip of p arm/short arm) in [[:File:Human chromosome 7 ideogram.svg|ideogram image]] (unit: pixel, example: 6 px)
* <math>qterPx</math>: Horizontal position of qter (tip of q arm/long arm) in [[:File:Human chromosome 7 ideogram.svg|ideogram image]] (unit: pixel, example: 1109 px)
* <math>ImageOriginalWidth</math>: Width of [[:File:Human chromosome 7 ideogram.svg|ideogram image]] (unit: pixel, example: 1125 px)

* <math>ImageShownWidth</math>: Shown width of ideogram image in Wikipedia page (unit: pixel, example: 300 px)
* <math>{\color{Blue}ArrowWidth^*}</math>: Calculated marker width proportional to the gene length. This is generally too small (e.g. 0.05px) and non integer. (unit: pixel)
* <math>{\color{Blue}ArrowWidth}</math>: Actual marker width shown in Wikipedia page. Minimum value is 2 and always integer (using [[ceiling function]]). To say, 2, 3, 4, 5...(unit: pixel)

By substituting the terms with example values, we get...

<math>PositionSetX = \Bigg\{ 6 + \bigg[(1109 - 6) \times \frac{\frac{({\color{Red}GeneStart} + {\color{Red}GeneEnd})}{2}}{{\color{Red}ChromosomeLength(n)}} \bigg] \Bigg\}  \times \frac{300}{1125} - \frac{{\color{Blue}ArrowWidth}}{2}</math>

<math>\qquad\qquad\qquad\ = \Bigg\{ 6 + \bigg[\frac{1103}{2} \times \frac{{\color{Red}GeneStart} + {\color{Red}GeneEnd}}{{\color{Red}ChromosomeLength(n)}} \bigg] \Bigg\}  \times \frac{300}{1125} - \frac{{\color{Blue}ArrowWidth}}{2}</math>

<math>\qquad\qquad\qquad\ = \bigg( 6 \times \frac{300}{1125} \bigg) + \bigg(\frac{1103}{2} \times \frac{300}{1125} \times \frac{{\color{Red}GeneStart} + {\color{Red}GeneEnd}}{{\color{Red}ChromosomeLength(n)}} \bigg) - \frac{{\color{Blue}ArrowWidth}}{2} </math>

<math>\qquad\qquad\qquad\ = \bigg(\frac{1103 \times 300}{2 \times 1125} \times \frac{{\color{Red}GeneStart} + {\color{Red}GeneEnd}}{{\color{Red}ChromosomeLength(n)}} \bigg) + \bigg( \frac{6 \times 300}{1125} \bigg) - \frac{{\color{Blue}ArrowWidth}}{2} </math>

<math>\qquad\qquad\qquad\ = \bigg(\frac{330900}{2250} \times \frac{{\color{Red}GeneStart} + {\color{Red}GeneEnd}}{{\color{Red}ChromosomeLength(n)}} \bigg) + \bigg( \frac{1800}{1125} \bigg) - \frac{{\color{Blue}ArrowWidth}}{2} </math>

<math>\qquad\qquad\qquad\ = \bigg(147.0666... \times \frac{{\color{Red}GeneStart} + {\color{Red}GeneEnd}}{{\color{Red}ChromosomeLength(n)}} \bigg) + 1.6 - \frac{{\color{Blue}ArrowWidth}}{2} </math>

<math>\qquad\qquad\qquad\ = \bigg( \frac{{\color{Red}GeneStart} + {\color{Red}GeneEnd}}{{\color{Red}ChromosomeLength(n)}} \times 147.0666... \bigg) + 1.6 - \frac{{\color{Blue}ArrowWidth}}{2} </math>

<math>{\color{Blue}ArrowWidth^*} =(1109 - 6) \times \frac{({\color{Red}GeneEnd} - {\color{Red}GeneStart})}{{\color{Red}ChromosomeLength(n)}}  \times \frac{300}{1125}</math>

<math>\qquad\qquad\quad\;\;\;\; =  \frac{({\color{Red}GeneEnd} - {\color{Red}GeneStart})}{{\color{Red}ChromosomeLength(n)}} \times \frac{1103 \times 300}{1125}</math>

<math>\qquad\qquad\quad\;\;\;\; =  \frac{({\color{Red}GeneEnd} - {\color{Red}GeneStart})}{{\color{Red}ChromosomeLength(n)}} \times \frac{330900}{1125}</math>

<math>\qquad\qquad\quad\;\;\;\; = \frac{({\color{Red}GeneEnd} - {\color{Red}GeneStart})}{{\color{Red}ChromosomeLength(n)}} \times 294.133..</math>

The form in the last lines of each equations are used in program. 

Actual calculation is like as follows for [[Sonic hedgehog|SHH gene]] ([[:wikidata:Q14860072]]).

Firstly we need to calculate arrow-width.

<math>{\color{Blue}ArrowWidth^*} = \frac{({\color{Red}155812273} - {\color{Red}155799986})}{{\color{Red}159345973}} \times 294.133..</math>

<math>\qquad\qquad\quad\;\;\;\; = \frac{{\color{Red}12287}  \times 294.133..}{{\color{Red}159345973}}</math>

<math>\qquad\qquad\quad\;\;\;\; = \frac{{\color{Red}3614012.171}}{{\color{Red}159345973}}</math>

<math>\qquad\qquad\quad\;\;\;\; = {\color{Red}0.022}</math>

Here we got 0.022px for marker image width for SHH gene. Is this wrong? No. This result is from tha fact that most genes are very short compared to whole chromosome length. If whole chromosome is shown in about 300px, most human genes (≒10kb) span only from 0.01px to 0.05px, depending on whole chromosome length. So third equation do job here. <math>({\color{Blue}ArrowWidth^*} < 2)</math>, to say <math>({\color{Red}0.022} < 2 )</math>, is true. Hence we get.... 

<math>{\color{Blue}ArrowWidth} = {\color{Red}2}</math>

Arrow-width is 2px. Then we can calculate arrow position using this value.

<math>PositionSetX = \bigg( \frac{{\color{Red}155799986} + {\color{Red}155812273}}{{\color{Red}159345973}} \times 147.0666... \bigg) +1.6 - \frac{{\color{Red}2}}{2} </math>

<math>\qquad\qquad\qquad\ = \bigg( \frac{{\color{Red}311612259}}{{\color{Red}159345973}} \times 147.0666... \bigg) +1.6 -{\color{Red}1} </math>

<math>\qquad\qquad\qquad\ = \bigg( {\color{Red}1.95557034253} \times 147.0666... \bigg) +{\color{Red}0.6} </math>

<math>\qquad\qquad\qquad\ = {\color{Red}287.599081336} +{\color{Red}0.6} </math>

<math>\qquad\qquad\qquad\ = {\color{Red}288.199081336} </math>

<math>\qquad\qquad\qquad\ \fallingdotseq {\color{Red}288.2} </math>

Thus we got answer. We should put the 2px width arrow (this -> [[File:Red rectangle 2x18.png|2px]] ) at 288.2px position.

Position coordinate is from the left (0 px) to the right (300 px).
}}

{{-}}

==4. See also==
Effort for reader-friendliness for general readers
*[[Wikipedia_talk:WikiProject_Medicine/Archive_97#Infobox_update_April_2017]]
Introductory gene textbook website by National Library of Medicine. It includes gene location data for each gene pages.
* [https://ghr.nlm.nih.gov/gene Genetics Home Reference - gene list]


==5. Test with Module==
at [[:Module:Infobox gene/sandbox2]]

<code><nowiki>{{#invoke:Infobox gene/sandbox2|getTemplateData}}</nowiki></code>

https://en.wikipedia.org/enwiki/w/index.php?title=Sonic_hedgehog&diff=prev&oldid=795122559

[[:Category:Pages with script errors]] - [https://en.wikipedia.org/enwiki/w/api.php?action=query&list=categorymembers&cmtitle=Category%3APages%20with%20script%20errors&cmprop=title&cmlimit=500&cmnamespace=0&format=xml Article namespace]

==6. On the width of the marker ==
{|class="wikitable floatright" width="325px" 
|+Human
!Basepairs !! Approx. width in Chr.1<br/>{{Nowrap|(Longest chromosome)}} !! Approx. width in Chr.21<br/>{{Nowrap|(Shortest chromosome)}}
|-
|valign="top" align="right"| 
|align="center"| [[File:Human chromosome 1 ideogram.svg|150px]]
|align="center"| [[File:Human chromosome 21 ideogram.svg|150px]]
|-
|valign="top" align="right"| 248.9Mb<br/>{{Nowrap|([[Chromosome 1 (human)|Chr.1]] length)}}
|valign="top" align="right"| 300px
|valign="top" align="right"| 1599px
|-
|valign="top" align="right"| 46.7Mb<br/>{{Nowrap|([[Chromosome 21 (human)|Chr.21]] length)}}
|valign="top" align="right"| 56px
|valign="top" align="right"| 300px
|-
|valign="top" align="right"| 5Mb
|valign="top" align="right"| 6px
|valign="top" align="right"| 32px
|-
|bgcolor="lightgreen" valign="top" align="right"| 2.3Mb<br/>{{Nowrap|('''Longest human gene length''')}}
|bgcolor="lightgreen" valign="top" align="right"| 2.8px
|bgcolor="red" valign="top" align="right"| 15px
|-
|valign="top" align="right"| 1.6Mb
|valign="top" align="right"| 2px
|valign="top" align="right"| 10.6px
|-
|valign="top" align="right"| 0.93Mb
|valign="top" align="right"| 1.1px
|valign="top" align="right"| 6px
|-
|valign="top" align="right"| 0.31Mb
|valign="top" align="right"| 0.38px
|valign="top" align="right"| 2px
|-
|bgcolor="lightgreen" valign="top" align="right"| 10kb<br/>{{Nowrap|('''Typical human gene length''')}}
|bgcolor="lightgreen" valign="top" align="right"| 0.012px
|bgcolor="lightgreen" valign="top" align="right"| 0.064px
|}
{|class="wikitable floatright" width="325px" 
|+Mouse
!Basepairs !! Approx. width in Chr.1<br/>{{Nowrap|(Longest chromosome)}} !! Approx. width in Chr.19<br/>{{Nowrap|(Shortest chromosome)}}
|-
|valign="top" align="right"| 
|align="center"| [[File:Ideogram of house mouse chromosome 1.svg|150px]]
|align="center"| [[File:Ideogram of house mouse chromosome 19.svg|150px]]
|-
|valign="top" align="right"| 195.4Mb<br/>{{Nowrap|(Chr.1 length)}}
|valign="top" align="right"| 300px
|valign="top" align="right"| 954.4px
|-
|valign="top" align="right"| 61.4Mb<br/>{{Nowrap|(Chr.19 length)}}
|valign="top" align="right"| 94.3px
|valign="top" align="right"| 300px
|-
|valign="top" align="right"| 3.9Mb
|valign="top" align="right"| 6px
|valign="top" align="right"| 19px
|-
|bgcolor="lightgreen" valign="top" align="right"| 2.3Mb<br/>{{Nowrap|('''Longest? mouse gene length''')}}
|bgcolor="lightgreen" valign="top" align="right"| 3.5px
|bgcolor="lightgreen" valign="top" align="right"| 11.2px
|-
|valign="top" align="right"| 1.3Mb
|valign="top" align="right"| 2px
|valign="top" align="right"| 6.3px
|-
|valign="top" align="right"| 1.2Mb
|valign="top" align="right"| 1.8px
|valign="top" align="right"| 6px
|-
|valign="top" align="right"| 0.4Mb
|valign="top" align="right"| 0.6px
|valign="top" align="right"| 2px
|-
|bgcolor="lightgreen" valign="top" align="right"| 10kb<br/>{{Nowrap|('''Typical mouse gene length''')}}
|bgcolor="lightgreen" valign="top" align="right"| 0.015px
|bgcolor="lightgreen" valign="top" align="right"| 0.049px
|}

Gene length is varies from one by one. So marker width also has to change page by page. Here I list up some data which are needed to think about marker width.

As result of some experiments, marker width must be at least 2px, because 1px marker is difficult to detect.

And largest marker width would be 15px (red area in the table at the right).

Length of the longest human genes are... http://www.cshlp.org/ghg5_all/section/gene.shtml
* [[Dystrophin]]      - 2.3 Mb at Chr.X
* [[CNTNAP2]]      - 2.3 Mb at Chr.7
* [[PTPRD]]      - 2.3 Mb at Chr.9
* [[RUNX1]]      - 1.2 Mb at Chr.21
* [[LARGE]]      - 760 kb at Chr.22

{|class="wikitable floatleft" width="325px"
|+ 1px width marker
|-
|colspan="4" |
<div align="center">
{{Superimpose2
  | base = Human chromosome 7 ideogram.svg
  | base_width = 300px
  | base_link = File:Human chromosome 7 ideogram.svg
  | float = Red rectangle 1x18.png
  | float_width = 1px
  | float_alt = an arrow
  | float_caption = 
  | link = File:Red rectangle 1x18.png
  | t = 
  | x = 286.2
  | y = 17
}}
</div>
|-
|}
{|class="wikitable floatleft" width="325px"
|+ 2px width marker
|-
|colspan="4" |
<div align="center">
{{Superimpose2
  | base = Human chromosome 7 ideogram.svg
  | base_width = 300px
  | base_link = File:Human chromosome 7 ideogram.svg
  | float = Vertical red bar.svg
  | float_width = 2px
  | float_alt = an arrow
  | float_caption = 
  | link = File:Vertical red rectangle2.svg
  | t = 
  | x = 286.2
  | y = 17
}}
</div>
|-
|}
{|class="wikitable floatleft" width="325px"
|+ 3px width marker
|-
|colspan="4" |
<div align="center">
{{Superimpose2
  | base = Human chromosome 7 ideogram.svg
  | base_width = 300px
  | base_link = File:Human chromosome 7 ideogram.svg
  | float = Red rectangle 3x18.png
  | float_width = 3px
  | float_alt = an arrow
  | float_caption = 
  | link = File:Red rectangle 3x18.png
  | t = 
  | x = 286.2
  | y = 17
}}
</div>
|-
|}
{|class="wikitable floatleft" width="325px"
|+ 4px width marker
|-
|colspan="4" |
<div align="center">
{{Superimpose2
  | base = Human chromosome 7 ideogram.svg
  | base_width = 300px
  | base_link = File:Human chromosome 7 ideogram.svg
  | float = Red rectangle 4x18.png
  | float_width = 4px
  | float_alt = an arrow
  | float_caption = 
  | link = File:Red rectangle 4x18.png
  | t = 
  | x = 286.2
  | y = 17
}}
</div>
|-
|}
{|class="wikitable floatleft" width="325px"
|+ 5px width marker
|-
|colspan="4" |
<div align="center">
{{Superimpose2
  | base = Human chromosome 7 ideogram.svg
  | base_width = 300px
  | base_link = File:Human chromosome 7 ideogram.svg
  | float = Red rectangle 5x18.png
  | float_width = 5px
  | float_alt = an arrow
  | float_caption = 
  | link = File:Red rectangle 5x18.png
  | t = 
  | x = 286.2
  | y = 17
}}
</div>
|-
|}
{|class="wikitable floatleft" width="325px"
|+ 6px width marker
|-
|colspan="4" |
<div align="center">
{{Superimpose2
  | base = Human chromosome 7 ideogram.svg
  | base_width = 300px
  | base_link = File:Human chromosome 7 ideogram.svg
  | float = Red rectangle 6x18.png
  | float_width = 6px
  | float_alt = an arrow
  | float_caption = 
  | link = File:Red rectangle 6x18.png
  | t = 
  | x = 286.2
  | y = 17
}}
</div>
|-
|}
{|class="wikitable floatleft" width="325px"
|+ 7px width marker
|-
|colspan="4" |
<div align="center">
{{Superimpose2
  | base = Human chromosome 7 ideogram.svg
  | base_width = 300px
  | base_link = File:Human chromosome 7 ideogram.svg
  | float = Red rectangle 7x18.png
  | float_width = 7px
  | float_alt = an arrow
  | float_caption = 
  | link = File:Red rectangle 7x18.png
  | t = 
  | x = 286.2
  | y = 17
}}
</div>
|-
|}
{|class="wikitable floatleft" width="325px"
|+ 8px width marker
|-
|colspan="4" |
<div align="center">
{{Superimpose2
  | base = Human chromosome 7 ideogram.svg
  | base_width = 300px
  | base_link = File:Human chromosome 7 ideogram.svg
  | float = Red rectangle 8x18.png
  | float_width = 8px
  | float_alt = an arrow
  | float_caption = 
  | link = File:Red rectangle 8x18.png
  | t = 
  | x = 286.2
  | y = 17
}}
</div>
|-
|}

{{-}}
{| class="wikitable" style="margin-left: auto; margin-right: auto;"
|-
! [[:commons:Template:Red rectangle series|Red rectangle series]] 
|-
|<gallery heights=18px  mode=packed>
File:Red rectangle 1x18.png|1x18
File:Red rectangle 2x18.png|2x18
File:Red rectangle 3x18.png|3x18
File:Red rectangle 4x18.png|4x18
File:Red rectangle 5x18.png|5x18
File:Red rectangle 6x18.png|6x18
File:Red rectangle 7x18.png|7x18
File:Red rectangle 8x18.png|8x18
</gallery>
<gallery heights=18px  mode=packed>
File:Red rectangle 9x18.png|9x18
File:Red rectangle 10x18.png|10x18
File:Red rectangle 11x18.png|11x18
File:Red rectangle 12x18.png|12x18
File:Red rectangle 13x18.png|13x18
File:Red rectangle 14x18.png|14x18
File:Red rectangle 15x18.png|15x18
File:Red rectangle 16x18.png|16x18
</gallery>
|}
{{-}}

==7. Ideograms ==
{| class="wikitable"
|-
! colspan="25" | [[:commons:Template:Human chromosome ideograms in svg|Human chromosome ideograms in svg]]
|- style="text-align: center; vertical-align: bottom;"
| style="width:30px; {{#ifeq:{{{1|}}}|1|background-color: #ccccee;|}}" | [[File:Human chromosome 1  ideogram.svg|30px]]<br/>1
| style="width:30px; {{#ifeq:{{{1|}}}|2|background-color: #ccccee;|}}" | [[File:Human chromosome 2  ideogram.svg|30px]]<br/>2
| style="width:30px; {{#ifeq:{{{1|}}}|3|background-color: #ccccee;|}}" | [[File:Human chromosome 3  ideogram.svg|30px]]<br/>3
| style="width:30px; {{#ifeq:{{{1|}}}|4|background-color: #ccccee;|}}" | [[File:Human chromosome 4  ideogram.svg|30px]]<br/>4
| style="width:30px; {{#ifeq:{{{1|}}}|5|background-color: #ccccee;|}}" | [[File:Human chromosome 5  ideogram.svg|30px]]<br/>5
| style="width:30px; {{#ifeq:{{{1|}}}|6|background-color: #ccccee;|}}" | [[File:Human chromosome 6  ideogram.svg|30px]]<br/>6
| style="width:30px; {{#ifeq:{{{1|}}}|7|background-color: #ccccee;|}}" | [[File:Human chromosome 7   ideogram.svg|30px]]<br/>7
| style="width:30px; {{#ifeq:{{{1|}}}|8|background-color: #ccccee;|}}" | [[File:Human chromosome 8  ideogram.svg|30px]]<br/>8
| style="width:30px; {{#ifeq:{{{1|}}}|9|background-color: #ccccee;|}}" | [[File:Human chromosome 9  ideogram.svg|30px]]<br/>9
| style="width:30px; {{#ifeq:{{{1|}}}|10|background-color: #ccccee;|}}" | [[File:Human chromosome 10 ideogram.svg|30px]]<br/>10
| style="width:30px; {{#ifeq:{{{1|}}}|11|background-color: #ccccee;|}}" | [[File:Human chromosome 11  ideogram.svg|30px]]<br/>11
| style="width:30px; {{#ifeq:{{{1|}}}|12|background-color: #ccccee;|}}" | [[File:Human chromosome 12  ideogram.svg|30px]]<br/>12
| style="width:30px; {{#ifeq:{{{1|}}}|13|background-color: #ccccee;|}}" | [[File:Human chromosome 13  ideogram.svg|30px]]<br/>13
| style="width:30px; {{#ifeq:{{{1|}}}|14|background-color: #ccccee;|}}" | [[File:Human chromosome 14  ideogram.svg|30px]]<br/>14
| style="width:30px; {{#ifeq:{{{1|}}}|15|background-color: #ccccee;|}}" | [[File:Human chromosome 15  ideogram.svg|30px]]<br/>15
| style="width:30px; {{#ifeq:{{{1|}}}|16|background-color: #ccccee;|}}" | [[File:Human chromosome 16  ideogram.svg|30px]]<br/>16
| style="width:30px; {{#ifeq:{{{1|}}}|17|background-color: #ccccee;|}}" | [[File:Human chromosome 17  ideogram.svg|30px]]<br/>17
| style="width:30px; {{#ifeq:{{{1|}}}|18|background-color: #ccccee;|}}" | [[File:Human chromosome 18  ideogram.svg|30px]]<br/>18
| style="width:30px; {{#ifeq:{{{1|}}}|19|background-color: #ccccee;|}}" | [[File:Human chromosome 19  ideogram.svg|30px]]<br/>19
| style="width:30px; {{#ifeq:{{{1|}}}|20|background-color: #ccccee;|}}" | [[File:Human chromosome 20  ideogram.svg|30px]]<br/>20
| style="width:30px; {{#ifeq:{{{1|}}}|21|background-color: #ccccee;|}}" | [[File:Human chromosome 21  ideogram.svg|30px]]<br/>21
| style="width:30px; {{#ifeq:{{{1|}}}|22|background-color: #ccccee;|}}" | [[File:Human chromosome 22  ideogram.svg|30px]]<br/>22
| style="width:30px; {{#ifeq:{{{1|}}}|X|background-color: #ccccee;|}}" | [[File:Human chromosome X ideogram.svg|30px]]<br/>X
| style="width:30px; {{#ifeq:{{{1|}}}|Y|background-color: #ccccee;|}}" | [[File:Human chromosome Y ideogram.svg|30px]]<br/>Y
|}
Currently used ideogram set is as above. If you want use different ideogram set, following 5 conditions must be met.
# 24 images are needed. (1-22 and XY)
# All 24 images must have same image size (same height and same width).
# Among all 24 images, pter (terminus of the p-arm, leftist point) and qter (terminus of the q-arm, rightest point) must be set at the same position.
# Banding pattern must be drawn in basepair-proportional style. Standard ideograms defined by [[ISCN]] are drawn based on actual visual appearance of stained chromosomes under microscope, is not basepair-proportional. (see the table below)
# All file names must have same format, changing only in chromosome number. For example, if you created chromosome 1 image named <code>MyPrettyNice_Chr1_Ideogram.png</code>, then the rest of file names should be as follows.
:<code>MyPrettyNice_Chr'''2'''_Ideogram.png</code>
:<code>MyPrettyNice_Chr'''3'''_Ideogram.png</code>
:<code>MyPrettyNice_Chr'''4'''_Ideogram.png</code>
:....
:<code>MyPrettyNice_Chr'''9'''_Ideogram.png</code>
:<code>MyPrettyNice_Chr'''10'''_Ideogram.png</code>
: ....
:<code>MyPrettyNice_Chr'''22'''_Ideogram.png</code>
:<code>MyPrettyNice_Chr'''X'''_Ideogram.png</code>
:<code>MyPrettyNice_Chr'''Y'''_Ideogram.png</code>

After these 5 conditions are met, you can switch current images into new images, by changing the part of the code where ideogram file name is defined.

{| class="wikitable"
|+ 2 types of ideogram (we should use bottom one)
!Ideogram
!Description
!Image
!The common
!Difference
!Cause
|-
|[[File:SHH location.png|200px]]<br/>{{nay}} We can not use this type
|Chr.7 ideogram of [[ISCN]] standard, which is drawn based on actual visual appearance of stained chromosome under microscope. 
|{{Nowrap|[[File:Schoolgirl Into Nurse- Medical Training in Britain, 1942 D8607.jpg|100px]][[File:Human male karyotpe high resolution - Chromosome 7 cropped.png|60px]]}}
|rowspan="2"| In both images, band order is the same. You can see that band color, from the left to right, is set in the following order...
*{{Color box|white|white}}
*{{Color box|lightgrey|light grey}}
*{{Color box|white|white}}
*{{Color box|black|black|#FFFFFF}}
*{{Color box|white|white}}
*{{Color box|black|black|#FFFFFF}}
* ....
This order is the same.
|rowspan="2"| The order is the same. But widths of each bands are different. The salient parts are highlighted in the image below. 
[[File:Comparison of different styles in ideogram.png|300px]]
The bands which are connected to each other are same band. You can see the difference of their width between the upper and the lower ideogram.
|rowspan="2"|The cause of this difference is that basepair-density is not homogeneous within the chromosome. In some part basepairs are densely packed, and in other part basepairs are sparsely packed.
|-
|[[File:Human chromosome 7 ideogram.svg|200px]]<br/>{{OK}} We can use this type
|Chr.7 ideogram drawn in basepair-proportional style. As far as I know, all [[genome browser]]s (e.g. Ensembl, UCSC and so on) use this style of ideograms.
|[[File:Chromosome DNA Gene.svg|160px]]
|}
{{-}}

==8. Forward and Reverse strands ==
https://www.biostars.org/p/210929/

https://www.biostars.org/p/3908/

http://seqanswers.com/forums/showthread.php?t=39388

In GRCh, as convention, direction from p-arm (short arm) to q-arm (long arm) is forward. The opposite direction is reverse.


From Nelson, Sarah C., et al. Trends in Genetics 28.8 (2012): 361-363.[http://www.cell.com/trends/genetics/fulltext/S0168-9525(12)00070-4]
<pre>In all human reference chromosomes, as for other eukaryotes, the plus (+) strand is defined as the strand with its 5' end at the tip of the short arm (Genome Reference Consortium, personal communication, March 27, 2012).</pre>

[[File:Twemoji 25b6.svg|14px|Forward strand]] Forward strand

[[File:Twemoji 25c0.svg|14px|Reverse strand]] Reverse strand

[[File:HSR 1996 II 3.4h.svg|16px|Forward strand]] Forward strand

[[File:HSR 1996 II 3.4g.svg|16px|Reverse strand]] Reverse strand

[[File:Fxemoji u25B6.svg|15px|Forward strand]] Forward strand

[[File:Fxemoji u25C0.svg|14px|Reverse strand]] Reverse strand

* [[Sense (molecular biology)]]
* [[Directionality (molecular biology)]]
* [[Upstream and downstream (DNA)]]
* [[Sense strand]]
* [[Coding strand]]
* [[Reference genome]]

==9. Others ==
If the following kind of technology is available, it's so nice.
* [[:meta:2016_Community_Wishlist_Survey/Categories/Multimedia#Allow_variants_of_an_image_to_be_derived_from_a_single_SVG]]
But currently it seems there are no this kind of technology.

Perhaps Graph extension can do something...
* [[:wikidata:Template:Extension:Graph]]
* https://github.com/vega/vega/wiki/Marks#image

==10. Pages for test==
* [[Dystrophin]] - long gene (2.3 Mb at Chr.X)
* [[RUNX1]] - long gene (1.2 Mb at Chr.21)
* [[Oct-4]] - has many Ensembl IDs
* [[Aprataxin]] - has many RefSeq IDs
* [[MT-ND1]] - mitochondrial gene
* [[IFNA8]] - has human data, but mouse data