# Load genotype file (note: header = T)
myG <- read.csv("gwaspr_myG_hmp.csv", header = T)
# Plot
mp <- gg_LD_Heatmap(
# Load genotype data
xG = myG,
# Select chromosome and region to analyse
chr = 6,
pos1 = 2500000,
pos2 = 4000000,
# Select a LD metric
metric = "R^2",
# Set the threshold for identifying linked markers
threshold = 0.9,
# Select markers to highlight
myMs = "Lcu.1GRN.Chr6p3269280",
# Set the size of the marker names on the x and y axes
axisTextSize = 3,
# prefix to trim from the marker name
nameTrim = "Lcu.1GRN.Chr6",
# Set custom title for plot
myTitle = "Lentil Diversity Panel",
# Select colors for the gradient scale
color.low = "white",
color.mid = "goldenrod1",
color.high = "darkred" )
# Save Plot
ggsave("figures/gg_LD_Heatmap_01.png",
mp[[1]], width = 12, height = 12, dpi = 600 )
# Save data
write.csv(mp[[2]], "figures/LD_Heatmap_data.csv", row.names = F)
read.csv("figures/LD_Heatmap_data.csv")[1:30,]
## SNP1 SNP2 R.2 Chr SNP1_d SNP2_d
## 1 p2525330 p2525330 0.0000000000 6 2525330 2525330
## 2 p2525330 p2556449 0.0009017462 6 2525330 2556449
## 3 p2525330 p2556737 0.4896666611 6 2525330 2556737
## 4 p2525330 p2557053 0.0050843582 6 2525330 2557053
## 5 p2525330 p2557113 0.1313557757 6 2525330 2557113
## 6 p2525330 p2558106 0.4561908009 6 2525330 2558106
## 7 p2525330 p2624430 0.3253504820 6 2525330 2624430
## 8 p2525330 p2624453 0.3463576884 6 2525330 2624453
## 9 p2525330 p2747121 0.2089890347 6 2525330 2747121
## 10 p2525330 p2747122 0.2089330650 6 2525330 2747122
## 11 p2525330 p2747161 0.0226736004 6 2525330 2747161
## 12 p2525330 p2747170 0.2914167831 6 2525330 2747170
## 13 p2525330 p2747202 0.0218454389 6 2525330 2747202
## 14 p2525330 p2747230 0.2890620222 6 2525330 2747230
## 15 p2525330 p2747250 0.0240439548 6 2525330 2747250
## 16 p2525330 p2747291 0.2394054943 6 2525330 2747291
## 17 p2525330 p2747305 0.3787211156 6 2525330 2747305
## 18 p2525330 p2747308 0.0203400873 6 2525330 2747308
## 19 p2525330 p2747315 0.2690796078 6 2525330 2747315
## 20 p2525330 p2747329 0.0026214735 6 2525330 2747329
## 21 p2525330 p2747332 0.2658085703 6 2525330 2747332
## 22 p2525330 p2747377 0.0043181052 6 2525330 2747377
## 23 p2525330 p2747395 0.2726070560 6 2525330 2747395
## 24 p2525330 p2747397 0.2198628404 6 2525330 2747397
## 25 p2525330 p2747428 0.0144815126 6 2525330 2747428
## 26 p2525330 p2747444 0.2404931749 6 2525330 2747444
## 27 p2525330 p2747446 0.2393698489 6 2525330 2747446
## 28 p2525330 p2747487 0.2296461371 6 2525330 2747487
## 29 p2525330 p2747494 0.3048660208 6 2525330 2747494
## 30 p2525330 p2747548 0.0227952146 6 2525330 2747548