## load libraries for running R
%load_ext rmagic
## for embedding figures
import matplotlib.pyplot as plt
%matplotlib inline
## a directory for putting figures & results into
! mkdir -p project_lantanoides/figures/
This analysis will use the data sets produced in Notebook2. We are interested in testing for introgression between lineages. We will use the ".loci" output file to perform D-statistic tests in pyRAD, and use the ".treemix.gz" output to test introgression in TreeMix.
Below is the tree inferred from this data set in RAxML.
%%R -w 400 -h 400
library(ape)
## 65,115 loci
## 5.6M bp alignment
## 44% missing data
lant_m4 <- read.tree("project_lantanoides/analyses_raxml/RAxML_bipartitions.lantanoides_c88d6m4p3")
tre <- ladderize(lant_m4)
plot(tre, edge.width=2)
nodelabels(tre$node.label, bg='grey')
First we will setup the input file with parameters and topologies over which to measure D
.
%%bash
## make a new directory for D-statistic tests
mkdir -p project_lantanoides/analysis_dtests/
## generate template params file
~/Dropbox/pyrad-github/pyRAD -D > project_lantanoides/analysis_dtests/template.D
## look at template
cat project_lantanoides/analysis_dtests/template.D
200 ## N bootstrap replicates test.loci ## loc/path to input .loci file dstats/test1_res ## output file path/name (no suffix) 4 ## which test: 4,part,foil,foilalt 2 ## N cores (execute jobs [lines below] in parallel 0 ## output ABBA/BABA loci to files (0=no,1,2=verbose) 0 ## output bootstrap Ds to files (0=no,1=yes) -----------------------------------------------------------
%%bash
## substitute new values into the template
sed -i "/## loc/c\project_lantanoides/outfiles/lantanoides_c88d6m4p3.loci ## loc/path " project_lantanoides/analysis_dtests/template.D
sed -i "/## output file/c\project_lantanoides/analysis_dtests/result ## output file " project_lantanoides/analysis_dtests/template.D
sed -i "/## N cores/c\16 ## N cores " project_lantanoides/analysis_dtests/template.D
## look at template
cat project_lantanoides/analysis_dtests/template.D
200 ## N bootstrap replicates project_lantanoides/outfiles/lantanoides_c88d6m4p3.loci ## loc/path project_lantanoides/analysis_dtests/result ## output file 4 ## which test: 4,part,foil,foilalt 16 ## N cores 0 ## output ABBA/BABA loci to files (0=no,1,2=verbose) 0 ## output bootstrap Ds to files (0=no,1=yes) -----------------------------------------------------------
## put samples into groups (taxa)
outgroups = ["plicatum_C1_MJDJP_12", "carlesii_D1_BP_001", "foetidum_D24_KFC_1942"]
nervosum = ["nervosum_C4_PWS_2298", "nervosum_C2_PWS_2288_2289"]
sympodiale = ["sympodiale_D18_KFC_1932"]
furcatum = ["furcatum_combined"]
lantanoides = ["lantanoides_D15_Beartown_2", "lantanoides_D14_Beartown_1",
"lantanoides_D_17_Mohawk_3","lantanoides_D16_Mohawk_2"]
def makeD4(P1,P2,P3,O,num,name,template):
stringout = ""
tests = []
i = 1
for p1 in P1:
for p2 in P2:
for p3 in P3:
if p1 != p2:
if set([p1,p2,p3]) not in tests:
stringout += "[%s]\t[%s]\t[%s]\t[%s]\t## test %i.%i\n" % (p1,p2,p3,",".join(O),num,i)
i += 1
tests.append(set([p1,p2,p3]))
! head -n 8 $template > "project_lantanoides/analysis_dtests/input."$num"."$name".txt"
! echo "$stringout" >> "project_lantanoides/analysis_dtests/input."$num"."$name".txt"
ostring = "/## output file/c\\project_lantanoides/analysis_dtests/out."+str(num)+"."+str(name)+" ## output file "
! sed -i "$ostring" "project_lantanoides/analysis_dtests/input."$num"."$name".txt"
##
makeD4(lantanoides,lantanoides,furcatum,outgroups,1,
"LLF","project_lantanoides/analysis_dtests/template.D")
makeD4(lantanoides,lantanoides,nervosum,outgroups,2,
"LLN","project_lantanoides/analysis_dtests/template.D")
makeD4(lantanoides,lantanoides,sympodiale,outgroups,3,
"LLS","project_lantanoides/analysis_dtests/template.D")
##
makeD4(lantanoides,furcatum,nervosum,outgroups,4,
"LFN","project_lantanoides/analysis_dtests/template.D")
makeD4(lantanoides,sympodiale,nervosum,outgroups,5,
"LFS","project_lantanoides/analysis_dtests/template.D")
##
makeD4(nervosum,nervosum,lantanoides,outgroups,6,
"NNL","project_lantanoides/analysis_dtests/template.D")
makeD4(nervosum,nervosum,sympodiale,outgroups,7,
"NNS","project_lantanoides/analysis_dtests/template.D")
makeD4(nervosum,nervosum,furcatum,outgroups,8,
"NNF","project_lantanoides/analysis_dtests/template.D")
%%bash
cat project_lantanoides/analysis_dtests/input.1.LLF.txt
200 ## N bootstrap replicates project_lantanoides/outfiles/lantanoides_c88d6m4p3.loci ## loc/path project_lantanoides/analysis_dtests/out.1.LLF ## output file 4 ## which test: 4,part,foil,foilalt 16 ## N cores 0 ## output ABBA/BABA loci to files (0=no,1,2=verbose) 0 ## output bootstrap Ds to files (0=no,1=yes) ----------------------------------------------------------- [lantanoides_D15_Beartown_2] [lantanoides_D14_Beartown_1] [furcatum_combined] [plicatum_C1_MJDJP_12,carlesii_D1_BP_001,foetidum_D24_KFC_1942] ## test 1.1 [lantanoides_D15_Beartown_2] [lantanoides_D_17_Mohawk_3] [furcatum_combined] [plicatum_C1_MJDJP_12,carlesii_D1_BP_001,foetidum_D24_KFC_1942] ## test 1.2 [lantanoides_D15_Beartown_2] [lantanoides_D16_Mohawk_2] [furcatum_combined] [plicatum_C1_MJDJP_12,carlesii_D1_BP_001,foetidum_D24_KFC_1942] ## test 1.3 [lantanoides_D14_Beartown_1] [lantanoides_D_17_Mohawk_3] [furcatum_combined] [plicatum_C1_MJDJP_12,carlesii_D1_BP_001,foetidum_D24_KFC_1942] ## test 1.4 [lantanoides_D14_Beartown_1] [lantanoides_D16_Mohawk_2] [furcatum_combined] [plicatum_C1_MJDJP_12,carlesii_D1_BP_001,foetidum_D24_KFC_1942] ## test 1.5 [lantanoides_D_17_Mohawk_3] [lantanoides_D16_Mohawk_2] [furcatum_combined] [plicatum_C1_MJDJP_12,carlesii_D1_BP_001,foetidum_D24_KFC_1942] ## test 1.6
## run tests
import glob
for test in range(1,9):
t = glob.glob("project_lantanoides/analysis_dtests/input."+str(test)+".*")[0]
print "running",t
stderr = ! ~/Dropbox/pyrad-github/pyRAD -d $t
running project_lantanoides/analysis_dtests/input.1.LLF.txt running project_lantanoides/analysis_dtests/input.2.LLN.txt running project_lantanoides/analysis_dtests/input.3.LLS.txt running project_lantanoides/analysis_dtests/input.4.LFN.txt running project_lantanoides/analysis_dtests/input.5.LFS.txt running project_lantanoides/analysis_dtests/input.6.NNL.txt running project_lantanoides/analysis_dtests/input.7.NNS.txt running project_lantanoides/analysis_dtests/input.8.NNF.txt
%%bash
echo -e "\n==== test 1 === furcatum into lantanoides?"
cut -f5-13 project_lantanoides/analysis_dtests/out.1.LLF.D4.txt
echo -e "\n==== test 2 === nervosum into lantanoides?"
cut -f5-13 project_lantanoides/analysis_dtests/out.2.LLN.D4.txt
echo -e "\n==== test 3 === sympodiale into lantanoides?"
cut -f5-13 project_lantanoides/analysis_dtests/out.3.LLS.D4.txt
echo -e "\n==== test 4 === nervosum into lant v furc"
cut -f5-13 project_lantanoides/analysis_dtests/out.4.LFN.D4.txt
echo -e "\n==== test 5 === sympodiale into lant v furc"
cut -f5-13 project_lantanoides/analysis_dtests/out.5.LFS.D4.txt
echo -e "\n==== test 6 === lantanoides into nervosum"
cut -f5-13 project_lantanoides/analysis_dtests/out.6.NNL.D4.txt
echo -e "\n==== test 7 === sympodiale into nervosum"
cut -f5-13 project_lantanoides/analysis_dtests/out.7.NNS.D4.txt
echo -e "\n==== test 8 === furcatum into nervosum"
cut -f5-13 project_lantanoides/analysis_dtests/out.8.NNF.D4.txt
==== test 1 === furcatum into lantanoides? D std(D) Z BABA ABBA nloci nboot pdisc notes 0.002 0.053 0.03 146.25 146.75 11307 200 0.03 test 1.1 -0.064 0.055 1.16 218.62 192.38 11845 200 0.04 test 1.2 0.040 0.054 0.74 159.50 172.75 11527 200 0.03 test 1.3 -0.113 0.039 2.87 357.62 284.88 19209 200 0.04 test 1.4 0.019 0.066 0.29 164.38 170.88 10989 200 0.03 test 1.5 0.130 0.036 3.59 268.62 349.12 19423 200 0.04 test 1.6 ==== test 2 === nervosum into lantanoides? D std(D) Z BABA ABBA nloci nboot pdisc notes 0.058 0.059 0.99 153.88 172.88 11739 200 0.03 test 2.1 0.041 0.063 0.66 121.88 132.38 10909 200 0.03 test 2.2 -0.126 0.054 2.32 219.00 170.00 12250 200 0.03 test 2.3 -0.054 0.063 0.85 189.12 169.88 11431 200 0.03 test 2.4 0.001 0.055 0.01 178.88 179.12 11866 200 0.03 test 2.5 -0.050 0.066 0.75 153.00 138.50 10949 200 0.03 test 2.6 -0.180 0.054 3.34 220.62 153.38 11723 200 0.03 test 2.7 -0.101 0.053 1.90 189.50 154.75 10933 200 0.03 test 2.8 -0.039 0.050 0.78 172.38 159.38 11319 200 0.03 test 2.9 -0.036 0.055 0.66 147.50 137.25 10479 200 0.03 test 2.10 0.091 0.046 1.99 163.62 196.38 11818 200 0.03 test 2.11 0.031 0.060 0.52 163.00 173.50 11058 200 0.03 test 2.12 ==== test 3 === sympodiale into lantanoides? D std(D) Z BABA ABBA nloci nboot pdisc notes 0.022 0.039 0.55 242.38 253.12 19262 200 0.03 test 3.1 -0.064 0.039 1.64 363.25 319.50 20148 200 0.04 test 3.2 0.004 0.041 0.10 291.50 294.00 19538 200 0.03 test 3.3 -0.113 0.038 2.95 357.62 284.88 19209 200 0.04 test 3.4 0.013 0.045 0.28 282.00 289.25 18618 200 0.03 test 3.5 0.130 0.039 3.36 268.62 349.12 19423 200 0.04 test 3.6 ==== test 4 === nervosum into lant v furc D std(D) Z BABA ABBA nloci nboot pdisc notes 0.016 0.043 0.39 455.00 470.25 6884 200 0.12 test 4.1 0.104 0.043 2.43 381.00 469.50 6292 200 0.12 test 4.2 0.043 0.039 1.12 425.25 463.50 6584 200 0.12 test 4.3 0.078 0.043 1.82 390.88 457.12 6085 200 0.12 test 4.4 0.056 0.040 1.38 454.12 507.88 6869 200 0.13 test 4.5 0.072 0.039 1.85 428.38 494.88 6357 200 0.13 test 4.6 0.099 0.036 2.72 413.50 504.25 6670 200 0.13 test 4.7 0.064 0.042 1.54 390.25 443.75 6084 200 0.12 test 4.8 ==== test 5 === sympodiale into lant v furc D std(D) Z BABA ABBA nloci nboot pdisc notes 0.034 0.030 1.16 741.62 794.38 11538 200 0.12 test 5.1 0.044 0.029 1.51 705.25 770.75 10743 200 0.13 test 5.2 0.030 0.029 1.04 707.12 750.88 10968 200 0.13 test 5.3 0.057 0.034 1.68 676.88 758.12 10243 200 0.13 test 5.4 0.059 0.028 2.12 726.50 817.25 11459 200 0.13 test 5.5 0.094 0.029 3.20 689.12 831.62 10770 200 0.13 test 5.6 0.056 0.030 1.89 684.75 766.00 11128 200 0.12 test 5.7 0.068 0.031 2.19 647.38 741.12 10331 200 0.12 test 5.8 ==== test 6 === lantanoides into nervosum D std(D) Z BABA ABBA nloci nboot pdisc notes 0.022 0.052 0.42 201.62 210.62 6918 200 0.06 test 6.1 -0.003 0.055 0.06 215.62 214.12 6615 200 0.06 test 6.2 0.013 0.057 0.24 211.50 217.25 6944 200 0.06 test 6.3 0.013 0.056 0.24 213.38 219.12 6676 200 0.06 test 6.4 ==== test 7 === sympodiale into nervosum D std(D) Z BABA ABBA nloci nboot pdisc notes 0.004 0.053 0.07 224.12 225.88 6867 200 0.06 test 7.1 ==== test 8 === furcatum into nervosum D std(D) Z BABA ABBA nloci nboot pdisc notes 0.003 0.068 0.05 151.50 152.50 4078 200 0.07 test 8.1
%%bash
mkdir -p project_lantanoides/analysis_treemix/
%%bash
echo -e "nerv\nfurc\nlant\nsymp\noutg" > project_lantanoides/analysis_treemix/poporder
## no admixture
treemix -i project_lantanoides/outfiles/testing_c88d6m10p3.treemix.gz \
-root outg \
-k 1 \
-o project_lantanoides/analysis_treemix/SNPs_m0 > project_lantanoides/analysis_treemix/logSm0
## 1 admixture edge
treemix -i project_lantanoides/outfiles/testing_c88d6m10p3.treemix.gz \
-root outg \
-k 1 \
-m 1 \
-o project_lantanoides/analysis_treemix/SNPs_m1 > project_lantanoides/analysis_treemix/logSm1
## 2 admixture edges
treemix -i project_lantanoides/outfiles/testing_c88d6m10p3.treemix.gz \
-root outg \
-k 1 \
-m 2 \
-o project_lantanoides/analysis_treemix/SNPs_m2 > project_lantanoides/analysis_treemix/logSm2
%%R
source("~/local/src/treemix/src/plotting_funcs.R")
%%R -h 400 -w 800
par(mfrow=c(1,2));
plot_tree("project_lantanoides/analysis_treemix/SNPs_m0", lwd=2)
plot_resid("project_lantanoides/analysis_treemix/SNPs_m0",
"project_lantanoides/analysis_treemix/poporder")
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 1 1 outg NOT_ROOT NOT_MIG TIP 33 NA NA NA NA 2 2 <NA> NOT_ROOT NOT_MIG NOT_TIP 32 3 1 16 2 3 3 lant NOT_ROOT NOT_MIG TIP 2 NA NA NA NA 4 4 symp NOT_ROOT NOT_MIG TIP 16 NA NA NA NA 5 15 furc NOT_ROOT NOT_MIG TIP 16 NA NA NA NA 6 16 <NA> NOT_ROOT NOT_MIG NOT_TIP 2 4 1 15 1 7 31 nerv NOT_ROOT NOT_MIG TIP 32 NA NA NA NA 8 32 <NA> NOT_ROOT NOT_MIG NOT_TIP 33 31 1 2 3 9 33 <NA> ROOT NOT_MIG NOT_TIP 33 1 1 32 4 V11 1 outg:0.0737969 2 (lant:0.0397762,(symp:0.0306949,furc:0.0355318):0.0185119):0.00736161 3 lant:0.0397762 4 symp:0.0306949 5 furc:0.0355318 6 (symp:0.0306949,furc:0.0355318):0.0185119 7 nerv:0.0432739 8 (nerv:0.0432739,(lant:0.0397762,(symp:0.0306949,furc:0.0355318):0.0185119):0.00736161):0.0737969 9 (outg:0.0737969,(nerv:0.0432739,(lant:0.0397762,(symp:0.0306949,furc:0.0355318):0.0185119):0.00736161):0.0737969); x y ymin ymax 1 0.07379690 0.9 0.8 1.0 2 0.08115851 0.4 0.0 0.6 3 0.12093471 0.5 0.4 0.6 4 0.13036531 0.3 0.2 0.4 5 0.13520221 0.1 0.0 0.2 6 0.09967041 0.2 0.0 0.4 7 0.11707080 0.7 0.6 0.8 8 0.07379690 0.6 0.0 0.8 9 0.00000000 0.8 0.0 1.0 [1] 0.0737969 0.1209347 0.1303653 0.1352022 0.1170708 [1] 0.003 [1] "mse 0.001844796" [1] 0.001844796 [1] "here" [1] "1 1 0" [1] "2 1 0.000854859999999999" [1] "2 2 0" [1] "3 1 -0.00070636" [1] "3 2 -0.00052454" [1] "3 3 0" [1] "4 1 -0.000148549999999999" [1] "4 2 0" [1] "4 3 0.00052454" [1] "4 4 0" [1] "5 1 0" [1] "5 2 -0.000330400000000002" [1] "5 3 0.000706400000000003" [1] "5 4 -0.000375899999999998" [1] "5 5 0" [1] "#FF0000" "#FF0C00" "#FF1900" "#FF2500" "#FF3200" "#FF3E00" "#FF4B00" [8] "#FF5700" "#FF6400" "#FF7000" "#FF7D00" "#FF8900" "#FF9600" "#FFA200" [15] "#FFAA00" "#FFB100" "#FFB800" "#FFBF00" "#FFC600" "#FFCC00" "#FFD300" [22] "#FFDA00" "#FFE100" "#FFE800" "#FFEF00" "#FFF500" "#FFFC00" "#FFFF0C" [29] "#FFFF20" "#FFFF33" "#FFFF47" "#FFFF5A" "#FFFF6D" "#FFFF81" "#FFFF94" [36] "#FFFFA7" "#FFFFBB" "#FFFFCE" "#FFFFE1" "#FFFFF5" "#F5FFF5" "#E1FFE1" [43] "#CEFFCE" "#BBFFBB" "#A7FFA7" "#94FF94" "#81FF81" "#6DFF6D" "#5AFF5A" [50] "#47FF47" "#33FF33" "#20FF20" "#0CFF0C" "#00F806" "#00E519" "#00D12D" [57] "#00BE40" "#00AB53" "#009767" "#00847A" "#00708E" "#005DA1" "#004AB4" [64] "#0036C8" "#0023DB" "#0010EE" "#0000FB" "#0000E8" "#0000D5" "#0000C1" [71] "#0000AE" "#00009A" "#000087" "#000074" "#000060" "#00004D" "#00003A" [78] "#000026" "#000013" "#000000" [1] 0.500 0.505 0.510 0.515 0.520 0.525 0.530 0.535 0.540 0.545 0.550 0.555 [13] 0.560 0.565 0.570 0.575 0.580 0.585 0.590 0.595 0.600 0.605 0.610 0.615 [25] 0.620 0.625 0.630 0.635 0.640 0.645 0.650 0.655 0.660 0.665 0.670 0.675 [37] 0.680 0.685 0.690 0.695 0.700 0.705 0.710 0.715 0.720 0.725 0.730 0.735 [49] 0.740 0.745 0.750 0.755 0.760 0.765 0.770 0.775 0.780 0.785 0.790 0.795 [61] 0.800 0.805 0.810 0.815 0.820 0.825 0.830 0.835 0.840 0.845 0.850 0.855 [73] 0.860 0.865 0.870 0.875 0.880 0.885 0.890 0.895 0.900 nerv furc lant symp outg 1 0.00000000 0.00085486 -0.00070636 -0.00014855 0.0000000 2 0.00085486 0.00000000 -0.00052454 0.00000000 -0.0003304 3 -0.00070636 -0.00052454 0.00000000 0.00052454 0.0007064 4 -0.00014855 0.00000000 0.00052454 0.00000000 -0.0003759 5 0.00000000 -0.00033040 0.00070640 -0.00037590 0.0000000
%%R -h 400 -w 800
par(mfrow=c(1,2))
plot_tree("project_lantanoides/analysis_treemix/SNPs_m1", lwd=2)
plot_resid("project_lantanoides/analysis_treemix/SNPs_m1",
"project_lantanoides/analysis_treemix/poporder")
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 1 1 outg NOT_ROOT NOT_MIG TIP 33 NA NA NA NA 2 2 <NA> NOT_ROOT NOT_MIG NOT_TIP 32 3 1 16 2 3 3 lant NOT_ROOT NOT_MIG TIP 2 NA NA NA NA 4 4 symp NOT_ROOT NOT_MIG TIP 16 NA NA NA NA 5 15 furc NOT_ROOT NOT_MIG TIP 16 NA NA NA NA 6 16 <NA> NOT_ROOT NOT_MIG NOT_TIP 2 4 1 15 1 7 31 nerv NOT_ROOT NOT_MIG TIP 32 NA NA NA NA 8 32 <NA> NOT_ROOT NOT_MIG NOT_TIP 33 31 1 2 3 9 33 <NA> ROOT NOT_MIG NOT_TIP 33 1 1 32 4 10 34 <NA> NOT_ROOT MIG NOT_TIP 16 15 NA NA NA V11 1 outg:0.0727818 2 (lant:0.0387222,(symp:0.030191,furc:0.0360352):0.0195665):0.00904034 3 lant:0.0387222 4 symp:0.030191 5 furc:0.0360352 6 (symp:0.030191,furc:0.0360352):0.0195665 7 nerv:0.0520042 8 (nerv:0.0520042,(lant:0.0387222,(symp:0.030191,furc:0.0360352):0.0195665):0.00904034):0.0727818 9 (outg:0.0727818,(nerv:0.0520042,(lant:0.0387222,(symp:0.030191,furc:0.0360352):0.0195665):0.00904034):0.0727818); 10 <NA> x y ymin ymax 1 0.07278180 0.9 0.8 1.0 2 0.08182214 0.4 0.0 0.6 3 0.12054434 0.5 0.4 0.6 4 0.13157964 0.3 0.2 0.4 5 0.13742384 0.1 0.0 0.2 6 0.10138864 0.2 0.0 0.4 7 0.11784481 0.7 0.6 0.8 8 0.07278180 0.6 0.0 0.8 9 0.00000000 0.8 0.0 1.0 10 0.12324604 NA 0.0 0.2 [1] "0.606558 0.10138864 0.13742384" [1] 0.0727818 0.1205443 0.1315796 0.1374238 0.1178448 [1] 0.003 [1] "mse 0.001844796" [1] 0.001844796 [1] "here" [1] "1 1 0" [1] "2 1 0" [1] "2 2 0" [1] "3 1 -3.81999999999987e-06" [1] "3 2 -0.000272590000000001" [1] "3 3 0" [1] "4 1 3.81999999999987e-06" [1] "4 2 -2.70000000000131e-07" [1] "4 3 0.00027285" [1] "4 4 0" [1] "5 1 0" [1] "5 2 0.0002729" [1] "5 3 3.60000000000291e-06" [1] "5 4 -0.0002764" [1] "5 5 0" [1] "#FF0000" "#FF0C00" "#FF1900" "#FF2500" "#FF3200" "#FF3E00" "#FF4B00" [8] "#FF5700" "#FF6400" "#FF7000" "#FF7D00" "#FF8900" "#FF9600" "#FFA200" [15] "#FFAA00" "#FFB100" "#FFB800" "#FFBF00" "#FFC600" "#FFCC00" "#FFD300" [22] "#FFDA00" "#FFE100" "#FFE800" "#FFEF00" "#FFF500" "#FFFC00" "#FFFF0C" [29] "#FFFF20" "#FFFF33" "#FFFF47" "#FFFF5A" "#FFFF6D" "#FFFF81" "#FFFF94" [36] "#FFFFA7" "#FFFFBB" "#FFFFCE" "#FFFFE1" "#FFFFF5" "#F5FFF5" "#E1FFE1" [43] "#CEFFCE" "#BBFFBB" "#A7FFA7" "#94FF94" "#81FF81" "#6DFF6D" "#5AFF5A" [50] "#47FF47" "#33FF33" "#20FF20" "#0CFF0C" "#00F806" "#00E519" "#00D12D" [57] "#00BE40" "#00AB53" "#009767" "#00847A" "#00708E" "#005DA1" "#004AB4" [64] "#0036C8" "#0023DB" "#0010EE" "#0000FB" "#0000E8" "#0000D5" "#0000C1" [71] "#0000AE" "#00009A" "#000087" "#000074" "#000060" "#00004D" "#00003A" [78] "#000026" "#000013" "#000000" [1] 0.500 0.505 0.510 0.515 0.520 0.525 0.530 0.535 0.540 0.545 0.550 0.555 [13] 0.560 0.565 0.570 0.575 0.580 0.585 0.590 0.595 0.600 0.605 0.610 0.615 [25] 0.620 0.625 0.630 0.635 0.640 0.645 0.650 0.655 0.660 0.665 0.670 0.675 [37] 0.680 0.685 0.690 0.695 0.700 0.705 0.710 0.715 0.720 0.725 0.730 0.735 [49] 0.740 0.745 0.750 0.755 0.760 0.765 0.770 0.775 0.780 0.785 0.790 0.795 [61] 0.800 0.805 0.810 0.815 0.820 0.825 0.830 0.835 0.840 0.845 0.850 0.855 [73] 0.860 0.865 0.870 0.875 0.880 0.885 0.890 0.895 0.900 nerv furc lant symp outg 1 0.00e+00 0.00000000 -0.00000382 0.00000382 0.0000000 2 0.00e+00 0.00000000 -0.00027259 -0.00000027 0.0002729 3 -3.82e-06 -0.00027259 0.00000000 0.00027285 0.0000036 4 3.82e-06 -0.00000027 0.00027285 0.00000000 -0.0002764 5 0.00e+00 0.00027290 0.00000360 -0.00027640 0.0000000
%%R -h 400 -w 800
par(mfrow=c(1,2))
plot_tree("project_lantanoides/analysis_treemix/SNPs_m2", lwd=2)
plot_resid("project_lantanoides/analysis_treemix/SNPs_m2",
"project_lantanoides/analysis_treemix/poporder")
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 1 1 outg NOT_ROOT NOT_MIG TIP 33 NA NA NA NA 2 2 <NA> NOT_ROOT NOT_MIG NOT_TIP 32 3 1 16 2 3 3 lant NOT_ROOT NOT_MIG TIP 2 NA NA NA NA 4 4 symp NOT_ROOT NOT_MIG TIP 16 NA NA NA NA 5 15 furc NOT_ROOT NOT_MIG TIP 16 NA NA NA NA 6 16 <NA> NOT_ROOT NOT_MIG NOT_TIP 2 4 1 15 1 7 31 nerv NOT_ROOT NOT_MIG TIP 32 NA NA NA NA 8 32 <NA> NOT_ROOT NOT_MIG NOT_TIP 33 31 1 2 3 9 33 <NA> ROOT NOT_MIG NOT_TIP 33 32 4 1 1 10 34 <NA> NOT_ROOT MIG NOT_TIP 16 15 NA NA NA 11 49 <NA> NOT_ROOT MIG NOT_TIP 33 1 NA NA NA V11 1 outg:0.145462 2 (lant:0.0381693,(symp:0.0270886,furc:0.0491967):0.022676):0.00966781 3 lant:0.0381693 4 symp:0.0270886 5 furc:0.0491967 6 (symp:0.0270886,furc:0.0491967):0.022676 7 nerv:0.0524267 8 (nerv:0.0524267,(lant:0.0381693,(symp:0.0270886,furc:0.0491967):0.022676):0.00966781):1.96937e-05 9 ((nerv:0.0524267,(lant:0.0381693,(symp:0.0270886,furc:0.0491967):0.022676):0.00966781):1.96937e-05,outg:0.145462); 10 <NA> 11 <NA> x y ymin ymax 1 0.1454616937 0.1 0.0 0.2 2 0.0096875037 0.6 0.2 0.8 3 0.0478568037 0.7 0.6 0.8 4 0.0594521037 0.5 0.4 0.6 5 0.0710897561 0.3 0.2 0.4 6 0.0323635037 0.4 0.2 0.6 7 0.0451364298 0.9 0.8 1.0 8 0.0000196937 0.8 0.2 1.0 9 0.0000000000 0.2 0.0 1.0 10 0.0474027348 NA 0.2 0.4 11 0.0000196937 NA 0.0 0.2 [1] "0.388348 0.0323635037 0.0710897561100534" [1] "0.000135387 0 0.1454616937" [1] 0.14546169 0.04785680 0.05945210 0.07108976 0.04513643 [1] 0.003 [1] "mse 0.001844796" [1] 0.001844796 [1] "here" [1] "1 1 0" [1] "2 1 0" [1] "2 2 0" [1] "3 1 9.99999999994061e-09" [1] "3 2 0" [1] "3 3 0" [1] "4 1 -9.99999999994061e-09" [1] "4 2 0" [1] "4 3 0" [1] "4 4 0" [1] "5 1 0" [1] "5 2 0" [1] "5 3 0" [1] "5 4 9.99999999994061e-08" [1] "5 5 0" [1] "#FF0000" "#FF0C00" "#FF1900" "#FF2500" "#FF3200" "#FF3E00" "#FF4B00" [8] "#FF5700" "#FF6400" "#FF7000" "#FF7D00" "#FF8900" "#FF9600" "#FFA200" [15] "#FFAA00" "#FFB100" "#FFB800" "#FFBF00" "#FFC600" "#FFCC00" "#FFD300" [22] "#FFDA00" "#FFE100" "#FFE800" "#FFEF00" "#FFF500" "#FFFC00" "#FFFF0C" [29] "#FFFF20" "#FFFF33" "#FFFF47" "#FFFF5A" "#FFFF6D" "#FFFF81" "#FFFF94" [36] "#FFFFA7" "#FFFFBB" "#FFFFCE" "#FFFFE1" "#FFFFF5" "#F5FFF5" "#E1FFE1" [43] "#CEFFCE" "#BBFFBB" "#A7FFA7" "#94FF94" "#81FF81" "#6DFF6D" "#5AFF5A" [50] "#47FF47" "#33FF33" "#20FF20" "#0CFF0C" "#00F806" "#00E519" "#00D12D" [57] "#00BE40" "#00AB53" "#009767" "#00847A" "#00708E" "#005DA1" "#004AB4" [64] "#0036C8" "#0023DB" "#0010EE" "#0000FB" "#0000E8" "#0000D5" "#0000C1" [71] "#0000AE" "#00009A" "#000087" "#000074" "#000060" "#00004D" "#00003A" [78] "#000026" "#000013" "#000000" [1] 0.500 0.505 0.510 0.515 0.520 0.525 0.530 0.535 0.540 0.545 0.550 0.555 [13] 0.560 0.565 0.570 0.575 0.580 0.585 0.590 0.595 0.600 0.605 0.610 0.615 [25] 0.620 0.625 0.630 0.635 0.640 0.645 0.650 0.655 0.660 0.665 0.670 0.675 [37] 0.680 0.685 0.690 0.695 0.700 0.705 0.710 0.715 0.720 0.725 0.730 0.735 [49] 0.740 0.745 0.750 0.755 0.760 0.765 0.770 0.775 0.780 0.785 0.790 0.795 [61] 0.800 0.805 0.810 0.815 0.820 0.825 0.830 0.835 0.840 0.845 0.850 0.855 [73] 0.860 0.865 0.870 0.875 0.880 0.885 0.890 0.895 0.900 nerv furc lant symp outg 1 0e+00 0 1e-08 -1e-08 0e+00 2 0e+00 0 0e+00 0e+00 0e+00 3 1e-08 0 0e+00 0e+00 0e+00 4 -1e-08 0 0e+00 0e+00 1e-07 5 0e+00 0 0e+00 1e-07 0e+00