SNPlotyper API
You can build a URL that will directly call the SNPlotyper analysis renderer.
Parameters:
View SNPlotyper strains and RGD IDs| Parameter | Valid Values | Default | Required | Example |
|---|---|---|---|---|
| chromosome | 1-20, X | None | Yes | chromosome=1 |
| start | Integer values | None | Yes | start=0 |
| end | Integer values | None | Yes | end=0 |
| group | rgd_common | None | No | group=rgd |
| show_qtl | 1, 0 | 0 | No | show_qtl=1 |
| show_rgd_genes | 1, 0 | 0 | No | show_rgd_genes=1 |
| landscape | 1, 0 | 0 | No | landscape=1 |
| hierarchical_cluster | 1, 0 | 0 | No | hierarchical_cluster=1 |
| filter_exclude |
-1 : No filtering 0 : Any of genotypes are missing x : x% of genotypes are missing, where x is an integer between 1 and 100 |
-1 | No | filter_exclude=50 |
| include_strain[] | When supplying a group, you can choose to include other strains not in the group by default by using RGD IDs. | - | Yes, if no group is specified | include_strain[]=629509 |
| exclude_strain[] | When supplying a group, you can choose to exclude strains included in the group by default by using RGD IDs. | - | No | exclude_strain[]=629509 |
| group_1[] | Choose how to group strains for visualization by using RGD IDs. | - | No | group_1[]=629509 |
| group_2[] | Choose how to group strains for visualization by using RGD IDs. | - | No | group_2[]=629509 |
| Strain Name | RGD ID |
|---|---|
| ACI/Eur | 1547869 |
| ACI/N | 10000 |
| ACI/Nkyo | 1302643 |
| ACI/NSlc | 1302670 |
| ACI/SegHsd | 737892 |
| ACI/Ztm | 737952 |
| ACI/ZtmKini | 2307299 |
| BB/OK | 61107 |
| BB/WorTky | 1302634 |
| BBDR.BBDP-(D4Mit6-D4Mit7)/2Rhw | 2306712 |
| BBDR.BBDP-(D4Mit6-D4Mit7)/3Rhw | 2306709 |
| BBDR.BBDP-(D4Mit6-D4Mit7)/Rhw | 728155 |
| BDE/Ztm | 737948 |
| BDII/Ztm | 737947 |
| BDIV/lfz | 737921 |
| BDIX/Han | 10005 |
| BDIX/Ifz | 2307318 |
| BDV/Ztm | 2307357 |
| BH/Ztm | 737920 |
| BN-Lx/Cub | 61117 |
| BN/HanKini | 2307298 |
| BN/NHsdMcwi | 61498 |
| BN/Rj | 631594 |
| BN/SsNHsd | 10008 |
| BN/SsNSlc | 1302631 |
| BN/Ztm | 1578713 |
| BS/Ztm | 737967 |
| BUF/SimRijHsd | 2307359 |
| BXH10 | 2307124 |
| BXH11 | 2307127 |
| BXH12-1 | 2307139 |
| BXH12-2 | 2307133 |
| BXH13 | 2307123 |
| BXH2 | 2307121 |
| BXH3 | 2307134 |
| BXH5 | 2307115 |
| BXH6 | 2307136 |
| BXH8 | 2307126 |
| BXH9 | 2307129 |
| CDR/Ygl | 1357181 |
| CDS/Ygl | 1357191 |
| COP/Crl | 1358153 |
| COP/OlaHsd | 10011 |
| DA.BI.RT1i-(D20Rat42-D20Rat31)/Rhd | 2307360 |
| DA.LEW.RT1f-(D20Wox15-D20Wox13)/Rhd | 2307301 |
| DA/HanKini | 2307156 |
| DA/OlaHsd | 734475 |
| DA/Slc | 61111 |
| DMY/Kyo | 1302645 |
| DON/Kyo | 1302719 |
| DRH/Seac | 625659 |
| E3/Han | 737913 |
| E3/Rhd | 634374 |
| F344/Crl | 737926 |
| F344/Han | 737893 |
| F344/NSlc | 1302627 |
| F344/NTac | 1566439 |
| F344/Stm | 1302686 |
| FHH/EurMcwi | 629509 |
| FXLE12/Stm | 1302602 |
| FXLE13/Stm | 1302665 |
| FXLE14/Stm | 1302615 |
| FXLE15/Stm | 1302673 |
| FXLE16/Stm | 1302619 |
| FXLE17/Stm | 1302708 |
| FXLE18/Stm | 1302682 |
| FXLE19/Stm | 1302690 |
| FXLE20/Stm | 1302633 |
| FXLE21/Stm | 1302607 |
| FXLE22/Stm | 1302683 |
| FXLE24/Stm | 1302611 |
| FXLE26/Stm | 1302598 |
| GAERS/Ins | 1554304 |
| GH/OmrMcwi | 1579686 |
| GK/Slc | 1554306 |
| GK/Swe | 10017 |
| HAA/FDSC | 1300432 |
| HTX/Kyo | 1302600 |
| HWY/Slc | 1302718 |
| HXB1 | 2307094 |
| HXB10 | 2307083 |
| HXB13 | 2307091 |
| HXB14 | 2307092 |
| HXB15 | 2307095 |
| HXB17 | 2307085 |
| HXB18 | 2307082 |
| HXB2 | 2307096 |
| HXB20 | 2307080 |
| HXB21 | 2307097 |
| HXB22 | 2307088 |
| HXB23 | 2307093 |
| HXB24 | 2307084 |
| HXB25 | 2307098 |
| HXB27 | 2307078 |
| HXB29 | 2307089 |
| HXB3 | 2307079 |
| HXB31 | 2307081 |
| HXB4 | 2307077 |
| HXB5 | 2307099 |
| HXB7 | 2307086 |
| IS/Kyo | 10018 |
| KDP/Tky | 724576 |
| KHR/Kyo | 1302639 |
| KND/Tky | 1302697 |
| LAA/FDSC | 1300433 |
| LE/Han | 737942 |
| LE/Stm | 629485 |
| LEA/Hok | 1302656 |
| LEC/Hok | 1302648 |
| LEJ/Hkm | 1302658 |
| LEW.1AV1/Kini | 2307300 |
| LEW/Crl | 737932 |
| LEW/Han | 737919 |
| LEW/Jms | 1559036 |
| LEW/NHsd | 1298093 |
| LEW/SsNSlc | 1302701 |
| LEXF10A/Stm | 1302621 |
| LEXF10B/Stm | 1302616 |
| LEXF10C/Stm | 1302612 |
| LEXF11/Stm | 1302638 |
| LEXF1A/Stm | 1302641 |
| LEXF1C/Stm | 1302666 |
| LEXF2A/Stm | 1302605 |
| LEXF2B/Stm | 1302710 |
| LEXF2C/Stm | 1302646 |
| LEXF3/Stm | 1302707 |
| LEXF4/Stm | 1302604 |
| LEXF5/Stm | 1302723 |
| LEXF6B/Stm | 1302617 |
| LEXF7A/Stm | 1302652 |
| LEXF7B/Stm | 1302649 |
| LEXF7C/Stm | 1302597 |
| LEXF8A/Stm | 1302653 |
| LEXF8D/Stm | 1302699 |
| LEXF9/Stm | 1302618 |
| LH/Mav | 10021 |
| LN/Mav | 10022 |
| LOU/CHan | 10023 |
| LUDW/OlaHsd | 2307358 |
| MES/Slc | 1302728 |
| MHS | 2307317 |
| MNS | 60992 |
| MNS/Gib | 10028 |
| MWF/Hsd | 737906 |
| NAR/SaU | 737969 |
| NE/Ins | 1559031 |
| NER/Kyo | 628486 |
| OM/Han | 10034 |
| OM/NSlc | 1302716 |
| PAR/Wsl | 737940 |
| PVG.1AV1/Kini | 2307157 |
| PVG/Seac | 1302722 |
| PXO1 | 2307138 |
| PXO10 | 2307132 |
| PXO2 | 2307356 |
| PXO3-1 | 2307355 |
| PXO3-2 | 2307116 |
| PXO4 | 2307135 |
| PXO5-1 | 2307128 |
| PXO5-2 | 2307117 |
| PXO6-1 | 2307137 |
| PXO6-2 | 2307125 |
| PXO6-3 | 2307130 |
| PXO7-1 | 2307119 |
| PXO7-2 | 2307120 |
| PXO8-1 | 2307122 |
| PXO8-2 | 2307131 |
| PXO9 | 2307118 |
| RCS/Kyo | 1302660 |
| RICO/Ngs | 1302624 |
| SBH/Ygl | 631572 |
| SBN/Ygl | 631573 |
| SER/Kyo | 1302695 |
| SHHF/Bbb | 2293770 |
| SHR.BN-(D18Rat32-D18Rat12)Ipcv | 2307087 |
| SHR.BN-(D8Mit5-D8Mgh6)/Ipcv | 61106 |
| SHR.BN10/Ipcv | 2307090 |
| SHR/1NCrl | 2307155 |
| SHR/Izm | 631577 |
| SHR/Kyo | 1302620 |
| SHR/Mol | 61110 |
| SHR/NCrl | 1357994 |
| SHR/NHsd | 724574 |
| SHR/OlaIpcv | 631848 |
| SHRSP | 61010 |
| SHRSP.SHRSR-(D1Rat134-Mt1-ps1)/Bbb | 2307169 |
| SHRSP.SHRSR-(Klk1-D1Mit3)/Bbb | 2307167 |
| SHRSP.WKY-(D2Mit21-D2Rat157)/Gcrc | 2301371 |
| SHRSP.WKY-(D2Mit5-D2Rat133)/Gcrc | 2301367 |
| SHRSP.WKY-(D2Rat13-D2Rat157)/Gcrc | 631278 |
| SHRSP.WKY-(D2Rat132-D2Rat53)/Gcrc | 2301369 |
| SHRSP.WKY-(D2Wox15-D2Rat133)/Gcrc | 2301368 |
| SHRSP.WKY-(D2Wox9-D2Mgh12)/Gcrc | 737863 |
| SHRSP/Ezo | 1559047 |
| SHRSP/Gcrc | 734759 |
| SHRSP/Izm | 631599 |
| SHRSP/Ngsk | 1559041 |
| SHRSR.SHRSP-(D1Rat134-Mt1-ps1)/Bbb | 2307161 |
| SHRSR.SHRSP-(Klk1-Mt1-ps1)/Bbb | 2307159 |
| SPRD/Han | 737962 |
| SR/JrHsd | 1582184 |
| SS/Jr | 10041 |
| SS/JrHsd | 1582190 |
| SS/JrHsdMcwi | 61499 |
| T2DN/Mcwi | 1579693 |
| THE | 68147 |
| TLE | 68148 |
| TM/Kyo | 1302623 |
| TO/Hkm | 1302655 |
| TRM/Kyo | 1302702 |
| TRMR/Kyo | 1302679 |
| W/Kyo | 1302672 |
| WAG/OlaHsd | 737946 |
| WAG/RijKyo | 10042 |
| WBN/KobSlc | 634369 |
| WF/Kop | 1302622 |
| WIAR/Iar | 2304222 |
| Wild1/Hubr | 1625284 |
| WKA/Seac | 1302694 |
| WKAH/HkmSlc | 1302687 |
| WKAH/Hok | 68184 |
| WKY.SHRSP-(Asgr1-Vamp2)/Bbb | 631601 |
| WKY/Bbb | 1581635 |
| WKY/Gcrc | 734760 |
| WKY/Han | 737895 |
| WKY/Izm | 631286 |
| WKY/NCrl | 1358112 |
| WKY/Nmna | 1302614 |
| WKYO | 70455 |
| WN/N | 10045 |
| WNA/Nem | 1302664 |
| WOKW/K | 737957 |
| WTC/Kyo | 10047 |
| ZI/Kyo | 1302726 |
Examples:
Basic
Display chromosome 1 from 120,000,000 to 130,000,000, with the "ACI/Eur" and "COP/Crl" strains.
http://snplotyper.mcw.edu/analyses/api_visualize?chromosome=1&end=130000000&start=120000000&include_strain[]=1547869&include_strain[]=1358153
Display chromosome 1 from 120,000,000 to 130,000,000, with the "ACI/Eur" and "COP/Crl" strains showing QTLs
http://snplotyper.mcw.edu/analyses/api_visualize?chromosome=1&end=130000000&start=120000000&include_strain[]=1547869&include_strain[]=1358153&show_qtl=1
Display chromosome 1 from 120,000,000 to 130,000,000, with the "ACI/Eur" and "COP/Crl" strains showing QTLs and RGD genes.
http://snplotyper.mcw.edu/analyses/api_visualize?chromosome=1&end=130000000&start=120000000&include_strain[]=1547869&include_strain[]=1358153&show_qtl=1&show_rgd_genes=1
Display chromosome 1 from 120,000,000 to 130,000,000, with the "ACI/Eur" and "COP/Crl" strains with "ACI/Eur" in group 1 and "COP/Crl" in group 2.
http://snplotyper.mcw.edu/analyses/api_visualize?chromosome=1&end=130000000&start=120000000&include_strain[]=1547869&include_strain[]=1358153&group_1[]=1547869&group_2[]=1358153
Using a strain group
Display the rgd_common strain group on chromosome 1 from 120,000,000 to 130,000,000.
http://snplotyper.mcw.edu/analyses/api_visualize?group=rgd_common&chromosome=1&end=130000000&start=120000000
Display the rgd strain group on chromosome 1 from 120,000,000 to 130,000,000, removing the "FHH/EurMcwi" and "SS/JrHsdMcwi" strains.
http://snplotyper.mcw.edu/analyses/api_visualize?group=rgd_common&chromosome=1&end=130000000&start=120000000&exclude_strain[]=629509&exclude_strain[]=61499
Display the rgd strain group on chromosome 1 from 120,000,000 to 130,000,000, adding the "ACI/Eur" and "COP/Crl" strains.
http://snplotyper.mcw.edu/analyses/api_visualize?group=rgd_common&chromosome=1&end=130000000&start=120000000&include_strain[]=1547869&include_strain[]=1358153
Current strain groups:
| Keyword | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
rgd_common |
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| Description | |||||||||||||||||||
These are a group of strains commonly used by researchers working on the Rat Genome Database. (RGD) |
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| Strains | |||||||||||||||||||
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