source: wurmlab.github.io/genomicscourse/2016-SIB/practicals/population_genetics/popgen
library(adegenet)
## Loading required package: ade4
##
## /// adegenet 2.1.0 is loaded ////////////
##
## > overview: '?adegenet'
## > tutorials/doc/questions: 'adegenetWeb()'
## > bug reports/feature requests: adegenetIssues()
library(ggplot2)
# read in data (reduced to 10000 SNPs)
snp_matrix <- read.table("reduced_snp_matrix.txt")
# read in loci positions
loci <- read.table("loci_positions.txt", header=TRUE)
# create genlight object
snp <- new("genlight",
snp_matrix,
chromosome=loci$scaffold,
position=loci$position,
ploidy=as.integer(2),
pop=as.factor(c(rep("Shoe0",192), rep("Shoe1",96), rep("Shoe0",192),
rep("Shoe1",287))))
snp
## /// GENLIGHT OBJECT /////////
##
## // 767 genotypes, 10,000 binary SNPs, size: 4.5 Mb
## 0 (0 %) missing data
##
## // Basic content
## @gen: list of 767 SNPbin
## @ploidy: ploidy of each individual (range: 2-2)
##
## // Optional content
## @ind.names: 767 individual labels
## @loc.names: 10000 locus labels
## @chromosome: factor storing chromosomes of the SNPs
## @position: integer storing positions of the SNPs
## @pop: population of each individual (group size range: 383-384)
## @other: a list containing: elements without names
snp@ind.names
## [1] "Gen1_Shoe0_1" "Gen1_Shoe0_10" "Gen1_Shoe0_11"
## [4] "Gen1_Shoe0_12" "Gen1_Shoe0_13" "Gen1_Shoe0_14"
## [7] "Gen1_Shoe0_15" "Gen1_Shoe0_16" "Gen1_Shoe0_17"
## [10] "Gen1_Shoe0_18" "Gen1_Shoe0_19" "Gen1_Shoe0_2"
## [13] "Gen1_Shoe0_20" "Gen1_Shoe0_21" "Gen1_Shoe0_22"
## [16] "Gen1_Shoe0_23" "Gen1_Shoe0_24" "Gen1_Shoe0_25"
## [19] "Gen1_Shoe0_26" "Gen1_Shoe0_27" "Gen1_Shoe0_28"
## [22] "Gen1_Shoe0_29" "Gen1_Shoe0_3" "Gen1_Shoe0_30"
## [25] "Gen1_Shoe0_31" "Gen1_Shoe0_32" "Gen1_Shoe0_33"
## [28] "Gen1_Shoe0_34" "Gen1_Shoe0_35" "Gen1_Shoe0_36"
## [31] "Gen1_Shoe0_37" "Gen1_Shoe0_38" "Gen1_Shoe0_39"
## [34] "Gen1_Shoe0_4" "Gen1_Shoe0_40" "Gen1_Shoe0_41"
## [37] "Gen1_Shoe0_42" "Gen1_Shoe0_43" "Gen1_Shoe0_44"
## [40] "Gen1_Shoe0_45" "Gen1_Shoe0_46" "Gen1_Shoe0_47"
## [43] "Gen1_Shoe0_48" "Gen1_Shoe0_49" "Gen1_Shoe0_5"
## [46] "Gen1_Shoe0_50" "Gen1_Shoe0_51" "Gen1_Shoe0_52"
## [49] "Gen1_Shoe0_53" "Gen1_Shoe0_54" "Gen1_Shoe0_55"
## [52] "Gen1_Shoe0_56" "Gen1_Shoe0_57" "Gen1_Shoe0_58"
## [55] "Gen1_Shoe0_59" "Gen1_Shoe0_6" "Gen1_Shoe0_60"
## [58] "Gen1_Shoe0_61" "Gen1_Shoe0_62" "Gen1_Shoe0_63"
## [61] "Gen1_Shoe0_64" "Gen1_Shoe0_65" "Gen1_Shoe0_66"
## [64] "Gen1_Shoe0_67" "Gen1_Shoe0_68" "Gen1_Shoe0_69"
## [67] "Gen1_Shoe0_7" "Gen1_Shoe0_70" "Gen1_Shoe0_71"
## [70] "Gen1_Shoe0_72" "Gen1_Shoe0_73" "Gen1_Shoe0_74"
## [73] "Gen1_Shoe0_75" "Gen1_Shoe0_76" "Gen1_Shoe0_77"
## [76] "Gen1_Shoe0_78" "Gen1_Shoe0_79" "Gen1_Shoe0_8"
## [79] "Gen1_Shoe0_80" "Gen1_Shoe0_81" "Gen1_Shoe0_82"
## [82] "Gen1_Shoe0_83" "Gen1_Shoe0_84" "Gen1_Shoe0_85"
## [85] "Gen1_Shoe0_86" "Gen1_Shoe0_87" "Gen1_Shoe0_88"
## [88] "Gen1_Shoe0_89" "Gen1_Shoe0_9" "Gen1_Shoe0_90"
## [91] "Gen1_Shoe0_91" "Gen1_Shoe0_92" "Gen1_Shoe0_93"
## [94] "Gen1_Shoe0_94" "Gen1_Shoe0_95" "Gen1_Shoe0_96"
## [97] "Gen2_Shoe0_1" "Gen2_Shoe0_10" "Gen2_Shoe0_11"
## [100] "Gen2_Shoe0_12" "Gen2_Shoe0_13" "Gen2_Shoe0_14"
## [103] "Gen2_Shoe0_15" "Gen2_Shoe0_16" "Gen2_Shoe0_17"
## [106] "Gen2_Shoe0_18" "Gen2_Shoe0_19" "Gen2_Shoe0_2"
## [109] "Gen2_Shoe0_20" "Gen2_Shoe0_21" "Gen2_Shoe0_22"
## [112] "Gen2_Shoe0_23" "Gen2_Shoe0_24" "Gen2_Shoe0_25"
## [115] "Gen2_Shoe0_26" "Gen2_Shoe0_27" "Gen2_Shoe0_28"
## [118] "Gen2_Shoe0_29" "Gen2_Shoe0_3" "Gen2_Shoe0_30"
## [121] "Gen2_Shoe0_31" "Gen2_Shoe0_32" "Gen2_Shoe0_33"
## [124] "Gen2_Shoe0_34" "Gen2_Shoe0_35" "Gen2_Shoe0_36"
## [127] "Gen2_Shoe0_37" "Gen2_Shoe0_38" "Gen2_Shoe0_39"
## [130] "Gen2_Shoe0_4" "Gen2_Shoe0_40" "Gen2_Shoe0_41"
## [133] "Gen2_Shoe0_42" "Gen2_Shoe0_43" "Gen2_Shoe0_44"
## [136] "Gen2_Shoe0_45" "Gen2_Shoe0_46" "Gen2_Shoe0_47"
## [139] "Gen2_Shoe0_48" "Gen2_Shoe0_49" "Gen2_Shoe0_5"
## [142] "Gen2_Shoe0_50" "Gen2_Shoe0_51" "Gen2_Shoe0_52"
## [145] "Gen2_Shoe0_53" "Gen2_Shoe0_54" "Gen2_Shoe0_55"
## [148] "Gen2_Shoe0_56" "Gen2_Shoe0_57" "Gen2_Shoe0_58"
## [151] "Gen2_Shoe0_59" "Gen2_Shoe0_6" "Gen2_Shoe0_60"
## [154] "Gen2_Shoe0_61" "Gen2_Shoe0_62" "Gen2_Shoe0_63"
## [157] "Gen2_Shoe0_64" "Gen2_Shoe0_65" "Gen2_Shoe0_66"
## [160] "Gen2_Shoe0_67" "Gen2_Shoe0_68" "Gen2_Shoe0_69"
## [163] "Gen2_Shoe0_7" "Gen2_Shoe0_70" "Gen2_Shoe0_71"
## [166] "Gen2_Shoe0_72" "Gen2_Shoe0_73" "Gen2_Shoe0_74"
## [169] "Gen2_Shoe0_75" "Gen2_Shoe0_76" "Gen2_Shoe0_77"
## [172] "Gen2_Shoe0_78" "Gen2_Shoe0_79" "Gen2_Shoe0_8"
## [175] "Gen2_Shoe0_80" "Gen2_Shoe0_81" "Gen2_Shoe0_82"
## [178] "Gen2_Shoe0_83" "Gen2_Shoe0_84" "Gen2_Shoe0_85"
## [181] "Gen2_Shoe0_86" "Gen2_Shoe0_87" "Gen2_Shoe0_88"
## [184] "Gen2_Shoe0_89" "Gen2_Shoe0_9" "Gen2_Shoe0_90"
## [187] "Gen2_Shoe0_91" "Gen2_Shoe0_92" "Gen2_Shoe0_93"
## [190] "Gen2_Shoe0_94" "Gen2_Shoe0_95" "Gen2_Shoe0_96"
## [193] "GenP2_Shoe1_1" "GenP2_Shoe1_10" "GenP2_Shoe1_11"
## [196] "GenP2_Shoe1_12" "GenP2_Shoe1_13" "GenP2_Shoe1_14"
## [199] "GenP2_Shoe1_15" "GenP2_Shoe1_16" "GenP2_Shoe1_17"
## [202] "GenP2_Shoe1_18" "GenP2_Shoe1_19" "GenP2_Shoe1_2"
## [205] "GenP2_Shoe1_20" "GenP2_Shoe1_21" "GenP2_Shoe1_22"
## [208] "GenP2_Shoe1_23" "GenP2_Shoe1_24" "GenP2_Shoe1_25"
## [211] "GenP2_Shoe1_26" "GenP2_Shoe1_27" "GenP2_Shoe1_28"
## [214] "GenP2_Shoe1_29" "GenP2_Shoe1_3" "GenP2_Shoe1_30"
## [217] "GenP2_Shoe1_31" "GenP2_Shoe1_32" "GenP2_Shoe1_33"
## [220] "GenP2_Shoe1_34" "GenP2_Shoe1_35" "GenP2_Shoe1_36"
## [223] "GenP2_Shoe1_37" "GenP2_Shoe1_38" "GenP2_Shoe1_39"
## [226] "GenP2_Shoe1_4" "GenP2_Shoe1_40" "GenP2_Shoe1_41"
## [229] "GenP2_Shoe1_42" "GenP2_Shoe1_43" "GenP2_Shoe1_44"
## [232] "GenP2_Shoe1_45" "GenP2_Shoe1_46" "GenP2_Shoe1_47"
## [235] "GenP2_Shoe1_48" "GenP2_Shoe1_49" "GenP2_Shoe1_5"
## [238] "GenP2_Shoe1_50" "GenP2_Shoe1_51" "GenP2_Shoe1_52"
## [241] "GenP2_Shoe1_53" "GenP2_Shoe1_54" "GenP2_Shoe1_55"
## [244] "GenP2_Shoe1_56" "GenP2_Shoe1_57" "GenP2_Shoe1_58"
## [247] "GenP2_Shoe1_59" "GenP2_Shoe1_6" "GenP2_Shoe1_60"
## [250] "GenP2_Shoe1_61" "GenP2_Shoe1_62" "GenP2_Shoe1_63"
## [253] "GenP2_Shoe1_64" "GenP2_Shoe1_65" "GenP2_Shoe1_66"
## [256] "GenP2_Shoe1_67" "GenP2_Shoe1_68" "GenP2_Shoe1_69"
## [259] "GenP2_Shoe1_7" "GenP2_Shoe1_70" "GenP2_Shoe1_71"
## [262] "GenP2_Shoe1_72" "GenP2_Shoe1_73" "GenP2_Shoe1_74"
## [265] "GenP2_Shoe1_75" "GenP2_Shoe1_76" "GenP2_Shoe1_77"
## [268] "GenP2_Shoe1_78" "GenP2_Shoe1_79" "GenP2_Shoe1_8"
## [271] "GenP2_Shoe1_80" "GenP2_Shoe1_81" "GenP2_Shoe1_82"
## [274] "GenP2_Shoe1_83" "GenP2_Shoe1_84" "GenP2_Shoe1_85"
## [277] "GenP2_Shoe1_86" "GenP2_Shoe1_87" "GenP2_Shoe1_88"
## [280] "GenP2_Shoe1_89" "GenP2_Shoe1_9" "GenP2_Shoe1_90"
## [283] "GenP2_Shoe1_91" "GenP2_Shoe1_92" "GenP2_Shoe1_93"
## [286] "GenP2_Shoe1_94" "GenP2_Shoe1_95" "GenP2_Shoe1_96"
## [289] "Rol1_Shoe0_1" "Rol1_Shoe0_10" "Rol1_Shoe0_11"
## [292] "Rol1_Shoe0_12" "Rol1_Shoe0_13" "Rol1_Shoe0_14"
## [295] "Rol1_Shoe0_15" "Rol1_Shoe0_16" "Rol1_Shoe0_17"
## [298] "Rol1_Shoe0_18" "Rol1_Shoe0_19" "Rol1_Shoe0_2"
## [301] "Rol1_Shoe0_20" "Rol1_Shoe0_21" "Rol1_Shoe0_22"
## [304] "Rol1_Shoe0_23" "Rol1_Shoe0_24" "Rol1_Shoe0_25"
## [307] "Rol1_Shoe0_26" "Rol1_Shoe0_27" "Rol1_Shoe0_28"
## [310] "Rol1_Shoe0_29" "Rol1_Shoe0_3" "Rol1_Shoe0_30"
## [313] "Rol1_Shoe0_31" "Rol1_Shoe0_32" "Rol1_Shoe0_33"
## [316] "Rol1_Shoe0_34" "Rol1_Shoe0_35" "Rol1_Shoe0_36"
## [319] "Rol1_Shoe0_37" "Rol1_Shoe0_38" "Rol1_Shoe0_39"
## [322] "Rol1_Shoe0_4" "Rol1_Shoe0_40" "Rol1_Shoe0_41"
## [325] "Rol1_Shoe0_42" "Rol1_Shoe0_43" "Rol1_Shoe0_44"
## [328] "Rol1_Shoe0_45" "Rol1_Shoe0_46" "Rol1_Shoe0_47"
## [331] "Rol1_Shoe0_48" "Rol1_Shoe0_49" "Rol1_Shoe0_5"
## [334] "Rol1_Shoe0_50" "Rol1_Shoe0_51" "Rol1_Shoe0_52"
## [337] "Rol1_Shoe0_53" "Rol1_Shoe0_54" "Rol1_Shoe0_55"
## [340] "Rol1_Shoe0_56" "Rol1_Shoe0_57" "Rol1_Shoe0_58"
## [343] "Rol1_Shoe0_59" "Rol1_Shoe0_6" "Rol1_Shoe0_60"
## [346] "Rol1_Shoe0_61" "Rol1_Shoe0_62" "Rol1_Shoe0_63"
## [349] "Rol1_Shoe0_64" "Rol1_Shoe0_65" "Rol1_Shoe0_66"
## [352] "Rol1_Shoe0_67" "Rol1_Shoe0_68" "Rol1_Shoe0_69"
## [355] "Rol1_Shoe0_7" "Rol1_Shoe0_70" "Rol1_Shoe0_71"
## [358] "Rol1_Shoe0_72" "Rol1_Shoe0_73" "Rol1_Shoe0_74"
## [361] "Rol1_Shoe0_75" "Rol1_Shoe0_76" "Rol1_Shoe0_77"
## [364] "Rol1_Shoe0_78" "Rol1_Shoe0_79" "Rol1_Shoe0_8"
## [367] "Rol1_Shoe0_80" "Rol1_Shoe0_81" "Rol1_Shoe0_82"
## [370] "Rol1_Shoe0_83" "Rol1_Shoe0_84" "Rol1_Shoe0_85"
## [373] "Rol1_Shoe0_86" "Rol1_Shoe0_87" "Rol1_Shoe0_88"
## [376] "Rol1_Shoe0_89" "Rol1_Shoe0_9" "Rol1_Shoe0_90"
## [379] "Rol1_Shoe0_91" "Rol1_Shoe0_92" "Rol1_Shoe0_93"
## [382] "Rol1_Shoe0_94" "Rol1_Shoe0_95" "Rol1_Shoe0_96"
## [385] "Rol2_Shoe0_1" "Rol2_Shoe0_10" "Rol2_Shoe0_11"
## [388] "Rol2_Shoe0_12" "Rol2_Shoe0_13" "Rol2_Shoe0_14"
## [391] "Rol2_Shoe0_15" "Rol2_Shoe0_16" "Rol2_Shoe0_17"
## [394] "Rol2_Shoe0_18" "Rol2_Shoe0_19" "Rol2_Shoe0_2"
## [397] "Rol2_Shoe0_20" "Rol2_Shoe0_21" "Rol2_Shoe0_22"
## [400] "Rol2_Shoe0_23" "Rol2_Shoe0_24" "Rol2_Shoe0_25"
## [403] "Rol2_Shoe0_26" "Rol2_Shoe0_27" "Rol2_Shoe0_28"
## [406] "Rol2_Shoe0_29" "Rol2_Shoe0_3" "Rol2_Shoe0_30"
## [409] "Rol2_Shoe0_31" "Rol2_Shoe0_32" "Rol2_Shoe0_33"
## [412] "Rol2_Shoe0_34" "Rol2_Shoe0_35" "Rol2_Shoe0_36"
## [415] "Rol2_Shoe0_37" "Rol2_Shoe0_38" "Rol2_Shoe0_39"
## [418] "Rol2_Shoe0_4" "Rol2_Shoe0_40" "Rol2_Shoe0_41"
## [421] "Rol2_Shoe0_42" "Rol2_Shoe0_43" "Rol2_Shoe0_44"
## [424] "Rol2_Shoe0_45" "Rol2_Shoe0_46" "Rol2_Shoe0_47"
## [427] "Rol2_Shoe0_48" "Rol2_Shoe0_49" "Rol2_Shoe0_5"
## [430] "Rol2_Shoe0_50" "Rol2_Shoe0_51" "Rol2_Shoe0_52"
## [433] "Rol2_Shoe0_53" "Rol2_Shoe0_54" "Rol2_Shoe0_55"
## [436] "Rol2_Shoe0_56" "Rol2_Shoe0_57" "Rol2_Shoe0_58"
## [439] "Rol2_Shoe0_59" "Rol2_Shoe0_6" "Rol2_Shoe0_60"
## [442] "Rol2_Shoe0_61" "Rol2_Shoe0_62" "Rol2_Shoe0_63"
## [445] "Rol2_Shoe0_64" "Rol2_Shoe0_65" "Rol2_Shoe0_66"
## [448] "Rol2_Shoe0_67" "Rol2_Shoe0_68" "Rol2_Shoe0_69"
## [451] "Rol2_Shoe0_7" "Rol2_Shoe0_70" "Rol2_Shoe0_71"
## [454] "Rol2_Shoe0_72" "Rol2_Shoe0_73" "Rol2_Shoe0_74"
## [457] "Rol2_Shoe0_75" "Rol2_Shoe0_76" "Rol2_Shoe0_77"
## [460] "Rol2_Shoe0_78" "Rol2_Shoe0_79" "Rol2_Shoe0_8"
## [463] "Rol2_Shoe0_80" "Rol2_Shoe0_81" "Rol2_Shoe0_82"
## [466] "Rol2_Shoe0_83" "Rol2_Shoe0_84" "Rol2_Shoe0_85"
## [469] "Rol2_Shoe0_86" "Rol2_Shoe0_87" "Rol2_Shoe0_88"
## [472] "Rol2_Shoe0_89" "Rol2_Shoe0_9" "Rol2_Shoe0_90"
## [475] "Rol2_Shoe0_91" "Rol2_Shoe0_92" "Rol2_Shoe0_93"
## [478] "Rol2_Shoe0_94" "Rol2_Shoe0_95" "Rol2_Shoe0_96"
## [481] "Rollin2_Shoe1_1" "Rollin2_Shoe1_10" "Rollin2_Shoe1_11"
## [484] "Rollin2_Shoe1_12" "Rollin2_Shoe1_13" "Rollin2_Shoe1_14"
## [487] "Rollin2_Shoe1_15" "Rollin2_Shoe1_16" "Rollin2_Shoe1_17"
## [490] "Rollin2_Shoe1_18" "Rollin2_Shoe1_19" "Rollin2_Shoe1_2"
## [493] "Rollin2_Shoe1_20" "Rollin2_Shoe1_21" "Rollin2_Shoe1_22"
## [496] "Rollin2_Shoe1_23" "Rollin2_Shoe1_24" "Rollin2_Shoe1_25"
## [499] "Rollin2_Shoe1_26" "Rollin2_Shoe1_27" "Rollin2_Shoe1_28"
## [502] "Rollin2_Shoe1_29" "Rollin2_Shoe1_3" "Rollin2_Shoe1_30"
## [505] "Rollin2_Shoe1_31" "Rollin2_Shoe1_32" "Rollin2_Shoe1_33"
## [508] "Rollin2_Shoe1_34" "Rollin2_Shoe1_35" "Rollin2_Shoe1_36"
## [511] "Rollin2_Shoe1_37" "Rollin2_Shoe1_38" "Rollin2_Shoe1_39"
## [514] "Rollin2_Shoe1_4" "Rollin2_Shoe1_40" "Rollin2_Shoe1_41"
## [517] "Rollin2_Shoe1_42" "Rollin2_Shoe1_43" "Rollin2_Shoe1_44"
## [520] "Rollin2_Shoe1_45" "Rollin2_Shoe1_46" "Rollin2_Shoe1_47"
## [523] "Rollin2_Shoe1_48" "Rollin2_Shoe1_49" "Rollin2_Shoe1_5"
## [526] "Rollin2_Shoe1_50" "Rollin2_Shoe1_51" "Rollin2_Shoe1_52"
## [529] "Rollin2_Shoe1_53" "Rollin2_Shoe1_54" "Rollin2_Shoe1_55"
## [532] "Rollin2_Shoe1_56" "Rollin2_Shoe1_57" "Rollin2_Shoe1_58"
## [535] "Rollin2_Shoe1_59" "Rollin2_Shoe1_6" "Rollin2_Shoe1_60"
## [538] "Rollin2_Shoe1_61" "Rollin2_Shoe1_62" "Rollin2_Shoe1_63"
## [541] "Rollin2_Shoe1_64" "Rollin2_Shoe1_65" "Rollin2_Shoe1_66"
## [544] "Rollin2_Shoe1_67" "Rollin2_Shoe1_68" "Rollin2_Shoe1_69"
## [547] "Rollin2_Shoe1_7" "Rollin2_Shoe1_70" "Rollin2_Shoe1_71"
## [550] "Rollin2_Shoe1_72" "Rollin2_Shoe1_73" "Rollin2_Shoe1_74"
## [553] "Rollin2_Shoe1_75" "Rollin2_Shoe1_76" "Rollin2_Shoe1_77"
## [556] "Rollin2_Shoe1_78" "Rollin2_Shoe1_79" "Rollin2_Shoe1_8"
## [559] "Rollin2_Shoe1_80" "Rollin2_Shoe1_81" "Rollin2_Shoe1_82"
## [562] "Rollin2_Shoe1_83" "Rollin2_Shoe1_84" "Rollin2_Shoe1_85"
## [565] "Rollin2_Shoe1_86" "Rollin2_Shoe1_87" "Rollin2_Shoe1_88"
## [568] "Rollin2_Shoe1_89" "Rollin2_Shoe1_9" "Rollin2_Shoe1_90"
## [571] "Rollin2_Shoe1_91" "Rollin2_Shoe1_92" "Rollin2_Shoe1_93"
## [574] "Rollin2_Shoe1_94" "Rollin2_Shoe1_95" "VH1_Shoe1_1"
## [577] "VH1_Shoe1_10" "VH1_Shoe1_11" "VH1_Shoe1_12"
## [580] "VH1_Shoe1_13" "VH1_Shoe1_14" "VH1_Shoe1_15"
## [583] "VH1_Shoe1_16" "VH1_Shoe1_17" "VH1_Shoe1_18"
## [586] "VH1_Shoe1_19" "VH1_Shoe1_2" "VH1_Shoe1_20"
## [589] "VH1_Shoe1_21" "VH1_Shoe1_22" "VH1_Shoe1_23"
## [592] "VH1_Shoe1_24" "VH1_Shoe1_25" "VH1_Shoe1_26"
## [595] "VH1_Shoe1_27" "VH1_Shoe1_28" "VH1_Shoe1_29"
## [598] "VH1_Shoe1_3" "VH1_Shoe1_30" "VH1_Shoe1_31"
## [601] "VH1_Shoe1_32" "VH1_Shoe1_33" "VH1_Shoe1_34"
## [604] "VH1_Shoe1_35" "VH1_Shoe1_36" "VH1_Shoe1_37"
## [607] "VH1_Shoe1_38" "VH1_Shoe1_39" "VH1_Shoe1_4"
## [610] "VH1_Shoe1_40" "VH1_Shoe1_41" "VH1_Shoe1_42"
## [613] "VH1_Shoe1_43" "VH1_Shoe1_44" "VH1_Shoe1_45"
## [616] "VH1_Shoe1_46" "VH1_Shoe1_47" "VH1_Shoe1_48"
## [619] "VH1_Shoe1_49" "VH1_Shoe1_5" "VH1_Shoe1_50"
## [622] "VH1_Shoe1_51" "VH1_Shoe1_52" "VH1_Shoe1_53"
## [625] "VH1_Shoe1_54" "VH1_Shoe1_55" "VH1_Shoe1_56"
## [628] "VH1_Shoe1_57" "VH1_Shoe1_58" "VH1_Shoe1_59"
## [631] "VH1_Shoe1_6" "VH1_Shoe1_60" "VH1_Shoe1_61"
## [634] "VH1_Shoe1_62" "VH1_Shoe1_63" "VH1_Shoe1_64"
## [637] "VH1_Shoe1_65" "VH1_Shoe1_66" "VH1_Shoe1_67"
## [640] "VH1_Shoe1_68" "VH1_Shoe1_69" "VH1_Shoe1_7"
## [643] "VH1_Shoe1_70" "VH1_Shoe1_71" "VH1_Shoe1_72"
## [646] "VH1_Shoe1_73" "VH1_Shoe1_74" "VH1_Shoe1_75"
## [649] "VH1_Shoe1_76" "VH1_Shoe1_77" "VH1_Shoe1_78"
## [652] "VH1_Shoe1_79" "VH1_Shoe1_8" "VH1_Shoe1_80"
## [655] "VH1_Shoe1_81" "VH1_Shoe1_82" "VH1_Shoe1_83"
## [658] "VH1_Shoe1_84" "VH1_Shoe1_85" "VH1_Shoe1_86"
## [661] "VH1_Shoe1_87" "VH1_Shoe1_88" "VH1_Shoe1_89"
## [664] "VH1_Shoe1_9" "VH1_Shoe1_90" "VH1_Shoe1_91"
## [667] "VH1_Shoe1_92" "VH1_Shoe1_93" "VH1_Shoe1_94"
## [670] "VH1_Shoe1_95" "VH1_Shoe1_96" "VL1_Shoe1_1"
## [673] "VL1_Shoe1_10" "VL1_Shoe1_11" "VL1_Shoe1_12"
## [676] "VL1_Shoe1_13" "VL1_Shoe1_14" "VL1_Shoe1_15"
## [679] "VL1_Shoe1_16" "VL1_Shoe1_17" "VL1_Shoe1_18"
## [682] "VL1_Shoe1_19" "VL1_Shoe1_2" "VL1_Shoe1_20"
## [685] "VL1_Shoe1_21" "VL1_Shoe1_22" "VL1_Shoe1_23"
## [688] "VL1_Shoe1_24" "VL1_Shoe1_25" "VL1_Shoe1_26"
## [691] "VL1_Shoe1_27" "VL1_Shoe1_28" "VL1_Shoe1_29"
## [694] "VL1_Shoe1_3" "VL1_Shoe1_30" "VL1_Shoe1_31"
## [697] "VL1_Shoe1_32" "VL1_Shoe1_33" "VL1_Shoe1_34"
## [700] "VL1_Shoe1_35" "VL1_Shoe1_36" "VL1_Shoe1_37"
## [703] "VL1_Shoe1_38" "VL1_Shoe1_39" "VL1_Shoe1_4"
## [706] "VL1_Shoe1_40" "VL1_Shoe1_41" "VL1_Shoe1_42"
## [709] "VL1_Shoe1_43" "VL1_Shoe1_44" "VL1_Shoe1_45"
## [712] "VL1_Shoe1_46" "VL1_Shoe1_47" "VL1_Shoe1_48"
## [715] "VL1_Shoe1_49" "VL1_Shoe1_5" "VL1_Shoe1_50"
## [718] "VL1_Shoe1_51" "VL1_Shoe1_52" "VL1_Shoe1_53"
## [721] "VL1_Shoe1_54" "VL1_Shoe1_55" "VL1_Shoe1_56"
## [724] "VL1_Shoe1_57" "VL1_Shoe1_58" "VL1_Shoe1_59"
## [727] "VL1_Shoe1_6" "VL1_Shoe1_60" "VL1_Shoe1_61"
## [730] "VL1_Shoe1_62" "VL1_Shoe1_63" "VL1_Shoe1_64"
## [733] "VL1_Shoe1_65" "VL1_Shoe1_66" "VL1_Shoe1_67"
## [736] "VL1_Shoe1_68" "VL1_Shoe1_69" "VL1_Shoe1_7"
## [739] "VL1_Shoe1_70" "VL1_Shoe1_71" "VL1_Shoe1_72"
## [742] "VL1_Shoe1_73" "VL1_Shoe1_74" "VL1_Shoe1_75"
## [745] "VL1_Shoe1_76" "VL1_Shoe1_77" "VL1_Shoe1_78"
## [748] "VL1_Shoe1_79" "VL1_Shoe1_8" "VL1_Shoe1_80"
## [751] "VL1_Shoe1_81" "VL1_Shoe1_82" "VL1_Shoe1_83"
## [754] "VL1_Shoe1_84" "VL1_Shoe1_85" "VL1_Shoe1_86"
## [757] "VL1_Shoe1_87" "VL1_Shoe1_88" "VL1_Shoe1_89"
## [760] "VL1_Shoe1_9" "VL1_Shoe1_90" "VL1_Shoe1_91"
## [763] "VL1_Shoe1_92" "VL1_Shoe1_93" "VL1_Shoe1_94"
## [766] "VL1_Shoe1_95" "VL1_Shoe1_96"
head(snp@gen)
## [[1]]
## /// SNPBIN OBJECT /////////
## 10,000 SNPs coded as bits, size: 5.1 Kb
## Ploidy: 3
## 0 (0 %) missing data
##
## [[2]]
## /// SNPBIN OBJECT /////////
## 10,000 SNPs coded as bits, size: 5.1 Kb
## Ploidy: 3
## 0 (0 %) missing data
##
## [[3]]
## /// SNPBIN OBJECT /////////
## 10,000 SNPs coded as bits, size: 5.1 Kb
## Ploidy: 3
## 0 (0 %) missing data
##
## [[4]]
## /// SNPBIN OBJECT /////////
## 10,000 SNPs coded as bits, size: 5.1 Kb
## Ploidy: 3
## 0 (0 %) missing data
##
## [[5]]
## /// SNPBIN OBJECT /////////
## 10,000 SNPs coded as bits, size: 5.1 Kb
## Ploidy: 3
## 0 (0 %) missing data
##
## [[6]]
## /// SNPBIN OBJECT /////////
## 10,000 SNPs coded as bits, size: 5.1 Kb
## Ploidy: 3
## 0 (0 %) missing data
# snp@chromosome
# try to set ploidy...
ploidy(snp) <- as.integer(2)
Heatmap of genotypes
# heatmap of genotypes
glPlot(snp)
PCA
pca <- glPca(snp, nf=10)
# fast plot
scatter(pca, posi="bottomright")
# colored by population
cbpalette <- (c("#E69F00","black"))
#plot(pca$scores[,1], pca$scores[,2],
#col=snp@pop)
#legend("bottomright", legend=levels(snp@pop), col=levels(snp@pop))
s.class(pca$scores, pop(snp), grid=FALSE, col=cbpalette)
