Module:Infobox gene: Difference between revisions

Revision as of 11:40, 18 August 2017

Revision as of 13:32, 19 August 2017

Line 200:

--end

if (chr ~= "" and gstart ~= "" and gend ~= "") or (chr_mm ~= "" and gstart_mm ~= "" and gend_mm ~= "") then

p.renderGeneLocation(frame, chr, gstart, gend, db, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, ensembl_mm, name)

end

Line 677:

local label_gstart = "Start" --**lclz**

local label_gend = "End" --**lclz**

local tooltip_arrowSign = "Genomic ___location for "..name --**lclz**

local arrowSign_width = 14

if chr ~= "" and gstart ~= "" and gend ~= "" then

--Chromosome lengths are from GRCh38.p10 https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh38.p10

--This table is used only for calculating "Where should red-rectangle put?"

Line 709 ⟶ 710:

chrLengthTable["Y"] = 57227415

local chrLength = chrLengthTable[chr]

--Different languages have different word order.

local chrTextTable = {}--**lclz**

chrTextTable["1"] = "Chromosome 1 (human)"

chrTextTable["2"] = "Chromosome 2 (human)"

chrTextTable["3"] = "Chromosome 3 (human)"

chrTextTable["4"] = "Chromosome 4 (human)"

chrTextTable["5"] = "Chromosome 5 (human)"

chrTextTable["6"] = "Chromosome 6 (human)"

chrTextTable["7"] = "Chromosome 7 (human)"

chrTextTable["8"] = "Chromosome 8 (human)"

chrTextTable["9"] = "Chromosome 9 (human)"

chrTextTable["10"] = "Chromosome 10 (human)"

chrTextTable["11"] = "Chromosome 11 (human)"

chrTextTable["12"] = "Chromosome 12 (human)"

chrTextTable["13"] = "Chromosome 13 (human)"

chrTextTable["14"] = "Chromosome 14 (human)"

chrTextTable["15"] = "Chromosome 15 (human)"

chrTextTable["16"] = "Chromosome 16 (human)"

chrTextTable["17"] = "Chromosome 17 (human)"

chrTextTable["18"] = "Chromosome 18 (human)"

chrTextTable["19"] = "Chromosome 19 (human)"

chrTextTable["20"] = "Chromosome 20 (human)"

chrTextTable["21"] = "Chromosome 21 (human)"

chrTextTable["22"] = "Chromosome 22 (human)"

chrTextTable["X"] = "X chromosome (human)"

chrTextTable["Y"] = "Y chromosome (human)"

local chrText = chrTextTable[chr]

--about the calculation below, see https://en.wikipedia.org/wiki/User:Was_a_bee/Gene#3._Calculation_detail

local markerWidth = ((gend - gstart) * 294.133 )/ chrLength

Line 764 ⟶ 794:

:css('text-align', 'center')

:css('background-color', rowBGcolor)

:wikitext("[[File:Ideogram human chromosome "..chr..".svg|300px|Human chromosome "..chrchrText.."]]")

:done() --end td

:done() --end tr

Line 778 ⟶ 808:

:tag('span')

:attr('class', 'plainlinks')

:wikitext("[[Chromosome "..chrchrText.." (human)]]"..source_link_chr)

:done() --end span

:done() --end td

Line 789 ⟶ 819:

:wikitext("<div align=\"center\">")

:wikitext("<div style=\"position\: relative\; width\: 300px\;\">")

:wikitext("[[File:Human chromosome "..chr.." ideogram.svg|300px|Human chromosome "..chrchrText.."]]")

:wikitext("<div style=\"position\: absolute\; left\: "..arrowSignLocation.."px\; top\: 2px\; padding\: 0\;\">[[File:HSR 1996 II 3.5e.svg|"..arrowSign_width.."px|Genomic ___location for "..nametooltip_arrowSign.."]]</div>")

:wikitext("<div style=\"position\: absolute\; left\: "..markerLocation.."px\; top\: 19px\; padding\: 0\;\">[[File:Red rectangle "..markerWidth.."x18.png|"..markerWidth.."px|Genomic ___location for "..nametooltip_arrowSign.."]]</div>")

:wikitext("</div>")

:wikitext("</div>")

Line 843 ⟶ 873:

end

if chr_mm ~= "" and gstart_mm ~= "" and gend_mm ~= "" then

--Chromosome lengths are from GRCm38.p5 https://www.ncbi.nlm.nih.gov/grc/mouse/data?asm=GRCm38.p5

local chrLengthTable_mm = {}

Line 868 ⟶ 898:

chrLengthTable_mm["Y"] = 91744698

local chrLength_mm = chrLengthTable_mm[chr_mm]

--Different languages have different word order.

local chrTextTable_mm = {}--**lclz**

chrTextTable_mm["1"] = "Chromosome 1 (mouse)"

chrTextTable_mm["2"] = "Chromosome 2 (mouse)"

chrTextTable_mm["3"] = "Chromosome 3 (mouse)"

chrTextTable_mm["4"] = "Chromosome 4 (mouse)"

chrTextTable_mm["5"] = "Chromosome 5 (mouse)"

chrTextTable_mm["6"] = "Chromosome 6 (mouse)"

chrTextTable_mm["7"] = "Chromosome 7 (mouse)"

chrTextTable_mm["8"] = "Chromosome 8 (mouse)"

chrTextTable_mm["9"] = "Chromosome 9 (mouse)"

chrTextTable_mm["10"] = "Chromosome 10 (mouse)"

chrTextTable_mm["11"] = "Chromosome 11 (mouse)"

chrTextTable_mm["12"] = "Chromosome 12 (mouse)"

chrTextTable_mm["13"] = "Chromosome 13 (mouse)"

chrTextTable_mm["14"] = "Chromosome 14 (mouse)"

chrTextTable_mm["15"] = "Chromosome 15 (mouse)"

chrTextTable_mm["16"] = "Chromosome 16 (mouse)"

chrTextTable_mm["17"] = "Chromosome 17 (mouse)"

chrTextTable_mm["18"] = "Chromosome 18 (mouse)"

chrTextTable_mm["19"] = "Chromosome 19 (mouse)"

local chrText_mm = chrTextTable_mm[chr_mm]

--about the calculation below, see https://en.wikipedia.org/wiki/User:Was_a_bee/Gene#3._Calculation_detail

local markerWidth_mm = ((gend_mm - gstart_mm) * 294.133 )/ chrLength_mm

Line 919 ⟶ 973:

:css('text-align', 'center')

:css('background-color', rowBGcolor)

:wikitext("[[File:Ideogram house mouse chromosome "..chr_mm..".svg|260px|Mouse chromosome "..chr_mmchrText_mm.."]]")

:done() --end td

:done() --end tr

Line 933 ⟶ 987:

:tag('span')

:attr('class', 'plainlinks')

:wikitext("Chromosome "..chr_mm.." (mouse)"chrText_mm..source_link_chr_mm)

:done() --end span

:done() --end td

Line 944 ⟶ 998:

:wikitext("<div align=\"center\">")

:wikitext("<div style=\"position\: relative\; width\: 300px\;\">")

:wikitext("[[File:Ideogram of house mouse chromosome "..chr_mm..".svg|300px|Mouse chromosome "..chr_mmchrText_mm.."]]")

:wikitext("<div style=\"position\: absolute\; left\: "..arrowSignLocation_mm.."px\; top\: 2px\; padding\: 0\;\">[[File:HSR 1996 II 3.5e.svg|"..arrowSign_width.."px|Genomic ___location for "..nametooltip_arrowSign.."]]</div>")

:wikitext("<div style=\"position\: absolute\; left\: "..markerLocation_mm.."px\; top\: 19px\; padding\: 0\;\">[[File:Red rectangle "..markerWidth_mm.."x18.png|"..markerWidth_mm.."px|Genomic ___location for "..nametooltip_arrowSign.."]]</div>")

:wikitext("</div>")

:wikitext("</div>")