I have this data below called test. I am trying to plot this data using manhattan function in qqman library, but if you notice in the plot, it is not labelling all point below Pvalue < -log10(1e-08). What am I missing here?
library(qqman)
manhattan(test, main = "", ylim=c(0,15),
col = c("blue4", "orange3"),
suggestiveline = -log10(1e-06),
genomewideline = -log10(1e-08),
annotateTop = TRUE,
annotatePval = -log10(1e-08),
chrlabs = as.character(sort(unique(test$CHR))))
Data:
test <- structure(list(SNP = c("CSNK1G2", "MEIS2", "RP11-128A17.1", "SPPL2B",
"SPPL2B", "ZBTB10", "SDK1", "1:29115501:C:G", "DCBLD2", "DCBLD2",
"MINPP1", "RN7SL411P", "CSRP2BP", "POFUT1", "SAMHD1", "ARFGEF2",
"PCSK1", "NRCAM", "FTSJ3", "MTSS1", "ZBTB10", "VNN2", "C22orf23",
"TRIP11", "RP11-267M23.3", "RNF17", "LAD1", "GCAT", "DPP6", "MYRIP",
"COL14A1", "THUMPD3", "5:90519607:G:C", "LMF2", "2:130182303:G:C",
"RP11-378A13.1", "XRCC2", "NOP9", "PTPRR", "IKZF4", "SND1", "PER3",
"REXO1", "ZNF554", "1:37828266:GA:G", "COQ5", "DAGLB", "3:113869718:C:T",
"UBQLN1", "GCN1L1", "3:152340425:C:A", "RP11-96C23.10", "SH3BP2",
"ATRNL1", "MAP3K9", "CEP170B", "SOAT1", "RGSL1", "RGSL1", "RPL5",
"FOLH1B", "AC068799.1", "MSI1", "TRIAP1", "NCOR2", "POLE", "TNFAIP2",
"COCH", "ZFYVE26", "ELMSAN1", "KIF7", "PTX4", "LA16c-OS12.2",
"FLJ45079", "CCDC178", "MUM1", "AP3D1", "RN7SL202P", "POLQ",
"HLTF", "AHSG", "ITPR1", "SHQ1", "Metazoa_SRP", "MYL5", "ANXA6",
"PKHD1L1", "COL14A1", "TNKS", "RP11-195F19.29", "LA16c-390E6.3",
"PKD1", "CRYBG3", "ARID3C", "CGN", "G2E3", "KIF26A", "SI", "VPS13A",
"OLFM3"), P = c(1.459e-12, 3.993e-12, 3.993e-12, 2.925e-11, 2.932e-11,
1.599e-10, 5.258e-10, 8.619e-10, 9.423e-10, 9.423e-10, 1.377e-09,
1.415e-09, 1.734e-09, 1.734e-09, 1.734e-09, 1.734e-09, 1.759e-09,
1.98e-09, 2.554e-09, 3.798e-09, 6.174e-09, 6.569e-09, 1.55e-08,
1.899e-08, 2.218e-08, 2.485e-08, 2.776e-08, 2.796e-08, 3.455e-08,
3.904e-08, 5.134e-08, 5.333e-08, 5.357e-08, 5.687e-08, 6.479e-08,
6.9e-08, 6.901e-08, 7.179e-08, 7.28e-08, 7.375e-08, 7.408e-08,
7.733e-08, 7.814e-08, 8.17e-08, 1.019e-07, 1.061e-07, 1.068e-07,
1.172e-07, 1.189e-07, 1.205e-07, 1.211e-07, 1.217e-07, 1.217e-07,
1.218e-07, 1.22e-07, 1.239e-07, 1.243e-07, 1.243e-07, 1.243e-07,
1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07,
1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07,
1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07,
1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07,
1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07, 1.243e-07,
1.243e-07, 1.245e-07, 1.245e-07, 1.247e-07, 1.247e-07, 1.249e-07,
1.249e-07, 1.25e-07, 1.252e-07, 1.254e-07, 1.259e-07), CHR = c(19,
15, 15, 19, 19, 8, 7, 1, 3, 3, 10, 3, 20, 20, 20, 20, 5, 7, 17,
8, 8, 6, 22, 14, 8, 13, 1, 22, 7, 3, 8, 3, 5, 22, 2, 2, 7, 14,
12, 12, 7, 1, 19, 19, 1, 12, 7, 3, 9, 12, 3, 10, 4, 10, 14, 14,
1, 1, 1, 1, 11, 12, 12, 12, 12, 12, 14, 14, 14, 14, 15, 16, 16,
17, 18, 19, 19, 19, 3, 3, 3, 3, 3, 3, 4, 5, 8, 8, 8, 9, 16, 16,
3, 9, 1, 14, 14, 3, 9, 1), BP = c(1953357L, 37037001L, 37094404L,
2334772L, 2351704L, 80486958L, 4077071L, 29115501L, 98811473L,
98811485L, 87552289L, 40210113L, 18162024L, 32230868L, 36930902L,
48989666L, 96399107L, 108234727L, 63824712L, 124704342L, 80487332L,
132752654L, 37956695L, 91993921L, 94534777L, 24874294L, 201386508L,
37816581L, 154807181L, 40209992L, 120158188L, 9384525L, 90519607L,
50505437L, 130182303L, 218253844L, 152660792L, 24306548L, 70764560L,
56002806L, 128087016L, 7819427L, 1825726L, 2834416L, 37828266L,
120509934L, 6447649L, 113869718L, 83713065L, 120162755L, 152340425L,
87008531L, 2831832L, 115215944L, 70809013L, 104884202L, 179302620L,
182474354L, 182488987L, 92832097L, 89670555L, 117277892L, 120357950L,
120444886L, 124332440L, 132639181L, 103126688L, 30885788L, 67804167L,
73738854L, 89633246L, 1486462L, 190308L, 77881996L, 33266975L,
1356531L, 2115209L, 3918955L, 121490123L, 149071684L, 186620833L,
4683555L, 72848177L, 72922141L, 680597L, 151122844L, 109450979L,
120280088L, 9679900L, 34655657L, 1465246L, 2108561L, 97893057L,
34625661L, 151520093L, 30597650L, 104178576L, 165063524L, 77405807L,
101846861L)), row.names = c(135977L, 89108L, 89111L, 136668L,
136719L, 266871L, 252346L, 20439L, 206542L, 206543L, 39549L,
201043L, 173375L, 174747L, 176078L, 177956L, 230107L, 244948L,
121300L, 259465L, 266873L, 232530L, 187699L, 87423L, 267501L,
75719L, 12894L, 187625L, 249450L, 201042L, 259059L, 206062L,
229682L, 190471L, 152953L, 160353L, 249361L, 81933L, 71724L,
69236L, 245983L, 27397L, 135369L, 136925L, 22276L, 61367L, 254396L,
192020L, 278877L, 61243L, 196181L, 39522L, 212204L, 31288L, 85338L,
79906L, 10456L, 10807L, 10810L, 28627L, 57504L, 60879L, 61339L,
61351L, 62524L, 63596L, 79508L, 82184L, 85041L, 85741L, 96907L,
98641L, 99118L, 124968L, 128649L, 133175L, 136343L, 139848L,
192458L, 195816L, 198417L, 201965L, 205639L, 205643L, 214737L,
222732L, 258461L, 259099L, 267666L, 276638L, 98628L, 99960L,
206314L, 276618L, 4727L, 82139L, 79769L, 196857L, 278603L, 192L
), class = "data.frame")