TABLE 3.
R commands used to generate Figure 1.
| Scale | Operation | Command | Output |
| Regional plot | Lead SNP LD + triangle LD + directioned gene length + linking line | IntRegionalPlot(chr = 9,left = 94178074-200000,right = 94178074 + 200000,gtf = gtf,association = association,hapmap = hapmap_am368,hapmap_ld = hapmap_am368, threshold = 5, leadsnp_size = 2) | Figure 1A |
| LD color scale | IntRegionalPlot(chr = 9,left = 94178074-200000,right = 94178074 + 200000,gtf = gtf, association = association,hapmap = hapmap_ am368,hapmap_ld = hapmap_am368, threshold = 5,leadsnp_size = 2,color02 = “gray81”,color04 = “gray61”,color06 = “gray41”,color08 = “gray11”,color10 = “gray1”) | Figure 1B | |
| Triangle LD from another set of genotype data | IntRegionalPlot(chr = 9,left = 94178074-200000,right = 94178074 + 200000,gtf = gtf, association = association,hapmap = hapmap _am368,hapmap_ld = hapmap2,threshold = 5, leadsnp_size = 2) | Figure 1C | |
| Zoom-in or -out | IntRegionalPlot(chr = 9,left = 94178074-2000,right = 94178074 + 6000,gtf = gtf, association = association,hapmap = hapmap_am368,hapmap_ld = hapmap_ am368,threshold = 5,leadsnp_size = 2) | Figure 1D | |
| Single genic plot | Triangle LD + gene structure + linking line | IntGenicPlot(‘GRMZM2G170927_T01’, gtf,association = zmvpp1_association, hapmap = zmvpp1_hapmap,leadsnp = FALSE,triangleLD = TRUE,threshold = 8) | Figure 1E |
| Flanking sequence | IntGenicPlot(‘GRMZM2G170927_T01’,gtf, association = zmvpp1_association,hapmap = zmvpp1_hapmap,leadsnp = FALSE, triangleLD = TRUE, threshold = 8,up = 500,down = 600) | Figure 1F | |
| Highlight marker by shape and/or color | IntGenicPlot(‘GRMZM2G170927_T01’,gtf, association = zmvpp1_association,hapmap = zmvpp1_hapmap,leadsnp = FALSE, triangleLD = TRUE,threshold = 8,up = 500, down = 600,marker2highlight = marker2highlight) | Figure 1G | |
| Selected markers linking from association to LD | IntGenicPlot(‘GRMZM2G170927_T01’,gtf, association = zmvpp1_association,hapmap = zmvpp1_hapmap,leadsnp = FALSE,triangleLD = TRUE,threshold = 8,up = 500,down = 600, marker2highlight = marker2highlight,link2gene = marker2link,link2LD = marker2link) | Figure 1H |