hyphaltip/.gitignore

## .gitignore
.Rproj.user
.Rhistory
.RData
.Ruserdata

## draw_tree.R
#!/usr/bin/env R
library(ggtree)
library(dplyr)
library(tidyverse)
library(treedataverse)
library(ape)
tree<-read.tree("RVT_1matching_sequences.tree")
labelfix <- tibble(label = tree$tip.label) %>%
  mutate(label2 = str_replace(label,'#\\S+',''),
         species = str_replace(label,"_\\S+$",""))

tree <- full_join(tree, labelfix, by = "label") %>%
  mutate(old_label = label, label = label2)

fams1 <- read_tsv("RVT1_fams.tsv",col_types ='fid')
#fams <- read.table("RVT1_fams.tsv", sep="\t", stringsAsFactor=F)
#fams1 is the table I want to attach `x`

g1 <- ggplot(tree, aes(x, y)) + geom_tree() +
  geom_tiplab(aes(label = label, color=species),
              size=1,linesize=.5) + theme_tree() +
  scale_colour_brewer(palette = "Dark2")

g1

p <- g1 + geom_facet(panel = "Percentages",
               data = fams1, geom = geom_col,
               aes(x = percentage), orientation = 'y', width = 0.8) +
  theme_tree2()
pdf("tree_percentage.pdf")
p
ggsave("tree_percentage_gg.pdf",p,height=10)

#gheatmap(g1, fams, offset=8, width=1,
#         colnames=FALSE, legend_title="TE family") +
#  scale_x_ggtree() +
#  scale_y_continuous(expand=c(0, 0.3))


## RVT1_fams.tsv

          
            family
            n
            percentage

            
              EmaiTE_00001583_INT
              4606
              1.2098658124698642

            
              EmaiTE_00003084_INT
              3953
              1.180466728466515

            
              EmaiTE_00002448_INT
              3729
              1.1046748952813175

            
              EmaiTE_00002736_INT
              7645
              0.843423229290474

            
              EmaiTE_00002120_INT
              4851
              0.7875355040374232

            
              EmaiTE_00002179_INT
              2019
              0.7257274308207773

            
              EmaiTE_00003215_INT
              2334
              0.6388513420942799

            
              EmaiTE_00001907_INT
              1196
              0.5869870555039892

            
              EmaiTE_00002798_INT
              2035
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              EmaiTE_00002371_INT
              2948
              0.500422242717028

            
              EmaiTE_00003098_INT
              1272
              0.42289952537117886

            
              EmaiTE_00002725_INT
              1961
              0.3562131281683175

            
              EmaiTE_00001450_INT
              2227
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              EmaiTE_00002326_INT
              972
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              2617
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              1198
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              1045
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              855
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              1853
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              EmaiTE_00000912_INT
              2047
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              EmaiTE_00001159_INT
              618
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              EmaiTE_00001305_INT
              364
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              EmaiTE_00001392_INT
              699
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              660
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              534
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              1579
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              402
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              752
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              322
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              1583
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              332
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              430
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              715
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              McicTE_00001518_INT
              1407
              0.2383227331946674

            
              McicTE_00001800_INT
              1156
              0.21333932249934032

            
              McicTE_00001296_INT
              1078
              0.19849988553372724

            
              McicTE_00001922_INT
              1564
              0.17754499557776826

            
              McicTE_00001382_INT
              6514
              0.14802509978242212

            
              McicTE_00001389_INT
              1821
              0.12177328938447805

            
              McicTE_00001697_INT
              924
              0.11314387288505331

            
              McicTE_00001596_INT
              762
              0.07564800304232167

            
              McicTE_00001427_INT
              758
              0.05712621065729217

            
              McicTE_00001584_INT
              347
              0.05595298291012174

            
              McicTE_00001179_INT
              1025
              0.04696625180026955

            
              McicTE_00001462_INT
              282
              0.021665354983985582

            
              McicTE_00002124_INT
              244
              0.007575741385066496

            
              McicTE_00001063_INT
              25
              7.324277869758156e-4

            
              McicTE_00001586_INT
              15
              4.8264338167888223e-4

            
              McicTE_00002121_INT
              49
              4.7068811839766307e-4

            
              zradTE_00000793_INT
              3006
              1.579804049849814

            
              zradTE_00001097_INT
              1982
              1.1373337750949641

            
              zradTE_00001233_INT
              1936
              1.0795351242474924

            
              zradTE_00001102_INT
              2508
              0.9557649018935238

            
              zradTE_00000712_INT
              2588
              0.9137478783343929

            
              zradTE_00001178_INT
              1745
              0.7987182862221451

            
              zradTE_00001146_INT
              1119
              0.6375836213335327

            
              zradTE_00001201_INT
              1777
              0.6263830751222365

            
              zradTE_00000700_INT
              1719
              0.5466054993196288

            
              zradTE_00000685_INT
              1592
              0.45496926001170707

            
              zradTE_00001221_INT
              1432
              0.438097179080478

            
              zradTE_00000753_INT
              906
              0.4276283156646794

            
              zradTE_00001255_INT
              1568
              0.4015144693045419

            
              zradTE_00001091_INT
              867
              0.395687223587956

            
              zradTE_00000969_INT
              884
              0.37808552541526647

            
              zradTE_00000985_INT
              739
              0.3507690499391415

            
              zradTE_00000850_INT
              730
              0.3250378077422088

            
              zradTE_00000734_INT
              1086
              0.31856118361407043

            
              zradTE_00001017_INT
              686
              0.31038031851644055

            
              zradTE_00000730_INT
              398
              0.3074914028622084

            
              zradTE_00001038_INT
              684
              0.28265216223181727

            
              zradTE_00001054_INT
              614
              0.2752118777009224

            
              zradTE_00001052_INT
              574
              0.2741627351387788

            
              zradTE_00001049_INT
              860
              0.2686079836663359

            
              zradTE_00000745_INT
              561
              0.26065734839947174

            
              zradTE_00001145_INT
              340
              0.2507957578706205

            
              zradTE_00000778_INT
              237
              0.19564705396415

            
              zradTE_00001286_INT
              305
              0.19184150898370148

            
              zradTE_00001326_INT
              844
              0.1889201800199619

            
              zradTE_00000726_INT
              239
              0.1637317018685059

            
              zradTE_00001018_INT
              1018
              0.1538348380322495

            
              zradTE_00000744_INT
              230
              0.13841293492393197

            
              zradTE_00000933_INT
              309
              0.11632294671710151

            
              zradTE_00001195_INT
              170
              0.10800845616213972

            
              zradTE_00001239_INT
              147
              0.10778013299663912

            
              zradTE_00000901_INT
              233
              0.10076185704442873

            
              zradTE_00000980_INT
              224
              0.0835330708198463

            
              zradTE_00001295_INT
              352
              0.08208241633061851

            
              zradTE_00000910_INT
              274
              0.08140713904921454

            
              zradTE_00001149_INT
              413
              0.07914265626931591

            
              zradTE_00000972_INT
              262
              0.0656137539917388

            
              zradTE_00000845_INT
              174
              0.061916412265087

            
              zradTE_00001229_INT
              149
              0.05724508236549257

            
              zradTE_00001095_INT
              119
              0.0559796921845276

            
              zradTE_00000916_INT
              157
              0.04608044501668977

            
              zradTE_00000826_INT
              485
              0.033601797522660924

            
              zradTE_00001264_INT
              209
              0.03213461860113524

            
              zradTE_00001061_INT
              75
              0.0316063134339192

            
              zradTE_00001090_INT
              847
              0.026255416256074245

            
              zradTE_00000839_INT
              88
              0.02392292908171893

            
              zradTE_00001162_INT
              49
              0.017788551368673286

            
              zradTE_00001237_INT
              34
              0.016916410898643562

            
              zradTE_00001290_INT
              59
              0.016830452072940143

            
              zradTE_00001153_INT
              35
              0.015865043893690624

            
              zradTE_00001106_INT
              73
              0.012954837143997712

            
              zradTE_00000783_INT
              29
              0.011922695680468273

            
              zradTE_00001274_INT
              17
              0.0057465302203616305

            
              zradTE_00001213_INT
              21
              0.0043646745694509905

            
              zradTE_00001191_INT
              11
              0.003649675095023271

            
              zradTE_00000948_INT
              16
              0.0032410131731948058

## RVT_1matching_sequences.tree
((((EmaiTE_00001450_INT#LTR/Gypsy.g376.t1:0.29671,(EmaiTE_00002326_INT#LTR/Gypsy.g874.t1:0.00053,EmaiTE_00002451_INT#LTR/Gypsy.g952.t1:0.11007)0.947:0.08348)0.832:0.03689,(((EmaiTE_00001393_INT#LTR/Gypsy.g358.t1:0.03535,EmaiTE_00002803_INT#LTR/Gypsy.g1130.t1:0.08322)0.888:0.04914,(((((((EmaiTE_00002736_INT#LTR/Gypsy.g1105.t1:0.26127,(((((EmaiTE_00002922_INT#LTR/Gypsy.g1185.t1:0.18493,EmaiTE_00001616_INT#LTR/Gypsy.g469.t1:0.04257)0.847:0.04445,EmaiTE_00000821_INT#LTR/Gypsy.g23.t1:0.07409)0.750:0.03516,EmaiTE_00001610_INT#LTR/Gypsy.g463.t1:0.07367)0.347:0.00055,(EmaiTE_00002053_INT#LTR/Gypsy.g732.t1:0.02019,EmaiTE_00001177_INT#LTR/Gypsy.g225.t1:0.05252)0.772:0.06700)0.822:0.12379,(EmaiTE_00002346_INT#LTR/Gypsy.g883.t1:0.21347,(EmaiTE_00002269_INT#LTR/Gypsy.g846.t1:0.08031,(EmaiTE_00002348_INT#LTR/Gypsy.g886.t1:0.04974,EmaiTE_00003191_INT#LTR/Gypsy.g1337.t1:0.01433)0.745:0.01623)0.847:0.09896)0.642:0.07605)0.706:0.10087)0.839:0.14261,EmaiTE_00002798_INT#LTR/Gypsy.g1126.t1:0.33429)0.000:0.05269,EmusTE_00001175_INT#LTR/Gypsy.g220.t1:0.45381)0.916:0.18049,(zradTE_00001038_INT#LTR/Gypsy.g182.t1:0.28895,(((((zradTE_00001146_INT#LTR/Gypsy.g234.t1:0.24888,zradTE_00000969_INT#LTR/Gypsy.g156.t1:0.08079)0.639:0.02683,(zradTE_00001097_INT#LTR/Gypsy.g212.t1:0.00988,zradTE_00000734_INT#LTR/Gypsy.g37.t1:0.11815)0.703:0.04104)0.954:0.15076,zradTE_00001054_INT#LTR/Gypsy.g195.t1:0.32034)0.198:0.00054,zradTE_00001255_INT#LTR/Gypsy.g291.t1:0.18959)0.735:0.05185,EmusTE_00001628_INT#LTR/Gypsy.g364.t1:1.25001)0.583:0.06345)0.799:0.05623)0.985:0.27117,((EmusTE_00001618_INT#LTR/Gypsy.g363.t1:0.62822,(EmaiTE_00001705_INT#LTR/Gypsy.g524.t1:0.23251,((EmaiTE_00001389_INT#LTR/Gypsy.g353.t1:0.22192,zradTE_00000901_INT#LTR/Gypsy.g118.t1:0.71357)0.763:0.07886,(EmaiTE_00000933_INT#LTR/Gypsy.g103.t1:0.29030,((EmaiTE_00001611_INT#LTR/Gypsy.g464.t1:0.27415,((((EmusTE_00001043_INT#LTR/Gypsy.g175.t1:0.06633,EmusTE_00000537_INT#LTR/Gypsy.g28.t1:0.07249)0.962:0.10720,EmusTE_00000828_INT#LTR/Gypsy.g116.t1:0.06065)0.797:0.02824,(EmaiTE_00002066_INT#LTR/Gypsy.g742.t1:0.18077,(EmaiTE_00001215_INT#LTR/Gypsy.g247.t1:0.12647,EmaiTE_00003223_INT#LTR/Gypsy.g1365.t1:0.07536)0.839:0.06380)0.955:0.09349)0.583:0.02946,EmusTE_00001182_INT#LTR/Gypsy.g222.t1:0.14233)0.909:0.09684)0.038:0.06763,(EmusTE_00001989_INT#LTR/Gypsy.g459.t1:0.14774,EmusTE_00001682_INT#LTR/Gypsy.g381.t1:0.11755)0.972:0.18777)0.258:0.06753)0.841:0.06546)0.830:0.05973)0.275:0.04101)0.791:0.06545,zradTE_00000948_INT#LTR/Gypsy.g149.t1:0.31736)0.995:0.30646)0.730:0.07831,((((EmusTE_00000531_INT#LTR/Gypsy.g25.t1:0.12521,(McicTE_00001584_INT#LTR/Gypsy.g81.t1:0.36259,(((EmusTE_00001947_INT#LTR/Gypsy.g452.t1:0.06803,EmusTE_00001665_INT#LTR/Gypsy.g374.t1:0.05045)0.940:0.13076,(EmusTE_00001242_INT#LTR/Gypsy.g240.t1:0.11731,(EmaiTE_00002875_INT#LTR/Gypsy.g1163.t1:0.12396,(EmaiTE_00002626_INT#LTR/Gypsy.g1052.t1:0.04036,EmaiTE_00000913_INT#LTR/Gypsy.g94.t1:0.11893)0.754:0.02112)0.881:0.13877)0.468:0.05810)0.621:0.05966,((((EmaiTE_00001466_INT#LTR/Gypsy.g384.t1:0.21215,EmaiTE_00003028_INT#LTR/Gypsy.g1250.t1:0.16857)0.788:0.05541,(EmaiTE_00001809_INT#LTR/Gypsy.g582.t1:0.27194,EmaiTE_00002102_INT#LTR/Gypsy.g753.t1:0.34981)0.927:0.24887)0.752:0.01461,(EmaiTE_00001882_INT#LTR/Gypsy.g624.t1:0.12686,(EmaiTE_00001087_INT#LTR/Gypsy.g190.t1:0.15093,EmaiTE_00001631_INT#LTR/Gypsy.g485.t1:0.11635)0.116:0.01144)0.826:0.03497)0.879:0.05453,EmaiTE_00002856_INT#LTR/Gypsy.g1156.t1:0.18818)0.714:0.03165)0.808:0.06287)0.366:0.03201)0.954:0.13346,((((((EmusTE_00001252_INT#LTR/Gypsy.g244.t1:0.07578,(EmusTE_00000939_INT#LTR/Gypsy.g150.t1:0.06156,EmusTE_00001309_INT#LTR/Gypsy.g262.t1:0.04118)0.913:0.08692)0.868:0.06427,(EmusTE_00001653_INT#LTR/Gypsy.g371.t1:0.45911,(EmaiTE_00002035_INT#LTR/Gypsy.g721.t1:0.16478,EmaiTE_00003169_INT#LTR/Gypsy.g1327.t1:0.15945)0.882:0.10497)0.705:0.04477)0.965:0.12254,(((EmaiTE_00001091_INT#LTR/Gypsy.g192.t1:0.09592,(EmaiTE_00001802_INT#LTR/Gypsy.g578.t1:0.01625,(EmaiTE_00002182_INT#LTR/Gypsy.g802.t1:0.13226,(EmaiTE_00001720_INT#LTR/Gypsy.g540.t1:0.12329,(EmaiTE_00001633_INT#LTR/Gypsy.g487.t1:0.04702,EmaiTE_00002942_INT#LTR/Gypsy.g1199.t1:0.03952)0.261:0.01337)0.875:0.00055)0.631:0.01261)0.929:0.05920)0.355:0.02731,EmaiTE_00001164_INT#LTR/Gypsy.g220.t1:0.20709)0.883:0.06217,(EmaiTE_00001526_INT#LTR/Gypsy.g423.t1:0.12122,(EmaiTE_00001501_INT#LTR/Gypsy.g400.t1:0.03957,EmaiTE_00000966_INT#LTR/Gypsy.g122.t1:0.06151)0.675:0.02991)0.867:0.06069)0.847:0.05675)0.993:0.14457,((EmaiTE_00002447_INT#LTR/Gypsy.g946.t1:0.19093,EmaiTE_00002721_INT#LTR/Gypsy.g1090.t1:0.11914)0.945:0.22735,EmusTE_00001772_INT#LTR/Gypsy.g401.t1:0.30571)0.834:0.09640)0.643:0.01423,(((EmaiTE_00001564_INT#LTR/Gypsy.g432.t1:0.06123,EmaiTE_00001777_INT#LTR/Gypsy.g561.t1:0.11578)0.950:0.19725,(EmaiTE_00002170_INT#LTR/Gypsy.g793.t1:0.00053,EmaiTE_00002322_INT#LTR/Gypsy.g869.t1:0.22332)1.000:0.32089)0.962:0.16218,(EmaiTE_00002929_INT#LTR/Gypsy.g1189.t1:0.01424,(EmaiTE_00001968_INT#LTR/Gypsy.g671.t1:0.09822,EmaiTE_00001524_INT#LTR/Gypsy.g420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1:0.07408)0.985:0.10484,(((EmaiTE_00001084_INT#LTR/Gypsy.g189.t1:0.00055,EmaiTE_00002725_INT#LTR/Gypsy.g1095.t1:0.07968)0.735:0.01938,(EmaiTE_00001834_INT#LTR/Gypsy.g597.t1:0.02393,EmaiTE_00002047_INT#LTR/Gypsy.g728.t1:0.04844)0.789:0.01709)0.888:0.04917,(EmaiTE_00002510_INT#LTR/Gypsy.g977.t1:0.19976,EmaiTE_00003101_INT#LTR/Gypsy.g1282.t1:0.21068)0.900:0.09681)0.907:0.06618)0.998:0.20639)0.798:0.05137,(EmusTE_00001775_INT#LTR/Gypsy.g402.t1:0.24335,EmusTE_00002075_INT#LTR/Gypsy.g487.t1:0.16879)0.719:0.13122)0.925:0.10941)0.803:0.09124,(zradTE_00001213_INT#LTR/Gypsy.g268.t1:0.11910,zradTE_00001237_INT#LTR/Gypsy.g281.t1:0.03244)0.995:0.23043)0.665:0.06094)0.996:0.33852)0.391:0.12865,(((((EmaiTE_00002833_INT#LTR/Gypsy.g1145.t1:0.07323,EmaiTE_00002061_INT#LTR/Gypsy.g738.t1:0.08065)0.838:0.06326,(EmaiTE_00002185_INT#LTR/Gypsy.g805.t1:0.05186,EmaiTE_00001545_INT#LTR/Gypsy.g427.t1:0.00055)0.993:0.21484)0.931:0.15224,((((((EmusTE_00001743_INT#LTR/Gypsy.g393.t1:0.02916,EmusTE_00001115_INT#LTR/Gypsy.g204.t1:0.21499)0.645:0.02062,(EmusTE_00001938_INT#LTR/Gypsy.g449.t1:0.05329,EmusTE_00001217_INT#LTR/Gypsy.g234.t1:0.07084)0.900:0.00055)0.739:0.01532,EmusTE_00001583_INT#LTR/Gypsy.g351.t1:0.05813)0.999:0.17406,((EmusTE_00000576_INT#LTR/Gypsy.g41.t1:0.27177,(EmusTE_00001672_INT#LTR/Gypsy.g378.t1:0.04724,EmusTE_00001932_INT#LTR/Gypsy.g448.t1:0.06736)0.748:0.02280)0.798:0.03279,EmusTE_00002158_INT#LTR/Gypsy.g511.t1:0.06905)0.967:0.11773)0.647:0.03844,((EmaiTE_00003149_INT#LTR/Gypsy.g1310.t1:0.14801,EmaiTE_00001163_INT#LTR/Gypsy.g219.t1:0.05113)0.508:0.11060,((zradTE_00000712_INT#LTR/Gypsy.g24.t1:0.08022,zradTE_00001049_INT#LTR/Gypsy.g191.t1:0.25993)0.856:0.10731,(zradTE_00001221_INT#LTR/Gypsy.g272.t1:0.21738,(zradTE_00000700_INT#LTR/Gypsy.g20.t1:0.27731,zradTE_00001201_INT#LTR/Gypsy.g263.t1:0.29734)0.782:0.06940)0.877:0.06551)0.940:0.10259)0.872:0.06114)0.959:0.10317,zradTE_00000685_INT#LTR/Gypsy.g13.t1:0.32227)0.816:0.05566)0.760:0.07699,(EmaiTE_00001871_INT#LTR/Gypsy.g618.t1:5.98818,EmaiTE_00002940_INT#LTR/Gypsy.g1198.t1:0.37486)0.510:0.06194)0.531:0.06344,((zradTE_00001178_INT#LTR/Gypsy.g248.t1:0.43822,((EmusTE_00001239_INT#LTR/Gypsy.g238.t1:0.06766,(EmusTE_00001999_INT#LTR/Gypsy.g462.t1:0.14808,EmusTE_00001659_INT#LTR/Gypsy.g372.t1:0.05976)0.197:0.02266)0.998:0.23781,(EmaiTE_00002246_INT#LTR/Gypsy.g837.t1:0.15858,(EmaiTE_00000834_INT#LTR/Gypsy.g32.t1:0.01725,(EmaiTE_00001338_INT#LTR/Gypsy.g330.t1:0.12366,((EmaiTE_00001058_INT#LTR/Gypsy.g174.t1:0.10388,EmaiTE_00002448_INT#LTR/Gypsy.g948.t1:0.07068)0.746:0.03295,EmaiTE_00001630_INT#LTR/Gypsy.g483.t1:0.02858)0.755:0.02011)0.713:0.03612)0.888:0.06620)0.854:0.06081)0.783:0.04773)0.340:0.02317,EmaiTE_00002784_INT#LTR/Gypsy.g1119.t1:0.32415)0.305:0.00207)0.979:0.24110)0.958:0.22671)0.757:0.12414,((McicTE_00001814_LTR#LTR/Gypsy.g111.t1:0.38618,EmaiTE_00002255_INT#LTR/Gypsy.g843.t1:0.85170)0.392:0.44887,(EmaiTE_00001305_INT#LTR/Gypsy.g311.t1:0.23510,(((EmaiTE_00002414_INT#LTR/Gypsy.g931.t1:0.03841,(EmaiTE_00002653_INT#LTR/Gypsy.g1061.t1:0.03349,EmaiTE_00002377_INT#LTR/Gypsy.g908.t1:0.00842)0.659:0.04389)0.075:0.02002,EmaiTE_00000781_INT#LTR/Gypsy.g6.t1:0.13408)0.843:0.06339,(EmaiTE_00001159_INT#LTR/Gypsy.g217.t1:0.09028,(EmaiTE_00000957_INT#LTR/Gypsy.g118.t1:0.06984,EmaiTE_00001587_INT#LTR/Gypsy.g449.t1:0.05123)0.964:0.20531)0.843:0.08430)0.939:0.26098)0.628:0.11529)1.000:1.89055)0.789:0.10811)0.803:0.00054,EmaiTE_00000912_INT#LTR/Gypsy.g90.t1:0.24523)0.771:0.02954)0.904:0.02874,(((zradTE_00000916_INT#LTR/Gypsy.g125.t1:0.42837,EmusTE_00001261_INT#LTR/Gypsy.g247.t1:0.09713)0.745:0.08140,(zradTE_00001095_INT#LTR/Gypsy.g209.t1:0.16769,McicTE_00001239_INT#LTR/Gypsy.g43.t1:0.05486)0.857:0.08463)0.751:0.03318,(zradTE_00001239_INT#LTR/Gypsy.g282.t1:0.27629,(zradTE_00000933_INT#LTR/Gypsy.g141.t1:0.20275,zradTE_00000980_INT#LTR/Gypsy.g159.t1:0.05393)0.939:0.19079)0.863:0.12086)0.616:0.00834)0.217:0.00054,(zradTE_00001286_INT#LTR/Gypsy.g303.t1:0.15753,((((EmusTE_00001105_INT#LTR/Gypsy.g200.t1:0.15865,EmaiTE_00003201_INT#LTR/Gypsy.g1348.t1:0.16607)0.653:0.01021,(EmaiTE_00001307_INT#LTR/Gypsy.g313.t1:0.04040,(EmaiTE_00002735_INT#LTR/Gypsy.g1102.t1:0.04646,(EmaiTE_00003209_INT#LTR/Gypsy.g1354.t1:0.06991,EmaiTE_00002163_INT#LTR/Gypsy.g786.t1:0.06235)0.567:0.00055)0.827:0.01642)0.909:0.02712)0.327:0.01393,EmaiTE_00003140_INT#LTR/Gypsy.g1303.t1:0.06584)0.846:0.03351,(EmusTE_00001199_INT#LTR/Gypsy.g226.t1:0.00076,zradTE_00001106_INT#LTR/Gypsy.g219.t1:0.10694)0.225:0.18136)0.852:0.02932)0.822:0.02905,(((((EmaiTE_00003227_INT#LTR/Gypsy.g1367.t1:0.21775,EmaiTE_00001387_INT#LTR/Gypsy.g349.t1:0.20972)0.307:0.19281,EmaiTE_00001935_INT#LTR/Gypsy.g653.t1:0.05247)0.811:0.05841,zradTE_00000744_INT#LTR/Gypsy.g39.t1:0.21607)0.756:0.01645,((EmaiTE_00000847_INT#LTR/Gypsy.g40.t1:0.42175,(McicTE_00002382_INT#LTR/Gypsy.g173.t1:0.11010,(EmaiTE_00001583_INT#LTR/Gypsy.g445.t1:0.66534,EmaiTE_00001014_INT#LTR/Gypsy.g149.t1:0.01560)0.877:0.33701)0.842:0.14332)0.255:0.00051,(zradTE_00000839_INT#LTR/Gypsy.g84.t1:0.00056,zradTE_00001295_INT#LTR/Gypsy.g314.t1:0.40398)0.873:0.15612)0.894:0.06914)0.753:0.01712,((((zradTE_00000778_INT#LTR/Gypsy.g57.t1:0.07910,(zradTE_00001229_INT#LTR/Gypsy.g275.t1:0.05546,zradTE_00001290_INT#LTR/Gypsy.g311.t1:0.07997)0.752:0.02212)1.000:0.17686,(((((McicTE_00001518_INT#LTR/Gypsy.g72.t1:0.21225,(McicTE_00002038_INT#LTR/Gypsy.g136.t1:0.05660,McicTE_00001179_INT#LTR/Gypsy.g36.t1:0.11013)0.851:0.09164)0.566:0.06685,zradTE_00000753_INT#LTR/Gypsy.g51.t1:0.39020)0.640:0.02288,(((((((EmaiTE_00002179_INT#LTR/Gypsy.g798.t1:0.27420,EmaiTE_00002831_INT#LTR/Gypsy.g1144.t1:0.09376)0.905:0.08927,(EmusTE_00001377_INT#LTR/Gypsy.g286.t1:0.01461,EmusTE_00000950_INT#LTR/Gypsy.g157.t1:0.09074)0.814:0.00054)0.554:0.01380,EmusTE_00002150_INT#LTR/Gypsy.g509.t1:0.18020)0.187:0.00051,EmaiTE_00001127_INT#LTR/Gypsy.g201.t1:0.08969)0.881:0.01714,(((EmusTE_00001225_INT#LTR/Gypsy.g236.t1:0.09379,(EmusTE_00002189_INT#LTR/Gypsy.g526.t1:0.06736,(EmusTE_00000510_INT#LTR/Gypsy.g16.t1:0.12248,(EmusTE_00000588_INT#LTR/Gypsy.g43.t1:0.20657,(EmusTE_00001793_INT#LTR/Gypsy.g409.t1:0.07757,EmusTE_00000685_INT#LTR/Gypsy.g69.t1:0.03417)0.766:0.03968)0.213:0.00055)0.929:0.00054)0.808:0.02328)0.771:0.01365,EmusTE_00000528_INT#LTR/Gypsy.g23.t1:0.02882)0.317:0.02524,EmusTE_00001550_INT#LTR/Gypsy.g342.t1:0.00055)0.104:0.00078)0.931:0.04483,((EmaiTE_00003098_INT#LTR/Gypsy.g1281.t1:0.16830,(EmaiTE_00001631_INT#LTR/Gypsy.g484.t1:0.04663,EmaiTE_00003215_INT#LTR/Gypsy.g1362.t1:0.09627)0.400:0.02507)0.586:0.01483,EmaiTE_00002819_INT#LTR/Gypsy.g1137.t1:0.15497)0.881:0.07044)0.905:0.05015,((EmaiTE_00003084_INT#LTR/Gypsy.g1276.t1:0.10785,(EmaiTE_00000871_INT#LTR/Gypsy.g52.t1:0.06781,EmaiTE_00002698_INT#LTR/Gypsy.g1081.t1:0.10465)0.845:0.03871)0.968:0.10200,(McicTE_00001956_INT#LTR/Gypsy.g127.t1:0.15878,McicTE_00001922_INT#LTR/Gypsy.g120.t1:0.01469)0.736:0.02012)0.981:0.09941)0.465:0.01504)0.992:0.10482,((zradTE_00000793_INT#LTR/Gypsy.g64.t1:0.06375,(zradTE_00001264_INT#LTR/Gypsy.g295.t1:0.18320,zradTE_00001102_INT#LTR/Gypsy.g216.t1:0.03382)0.034:0.00762)0.984:0.13266,(((((EmusTE_00000962_INT#LTR/Gypsy.g158.t1:0.05033,(EmusTE_00000768_INT#LTR/Gypsy.g97.t1:0.04850,EmusTE_00001687_INT#LTR/Gypsy.g387.t1:0.14444)0.723:0.01340)0.462:0.00055,EmusTE_00002172_INT#LTR/Gypsy.g514.t1:0.04802)0.940:0.05546,(EmaiTE_00000836_INT#LTR/Gypsy.g35.t1:0.10724,((EmaiTE_00000891_INT#LTR/Gypsy.g73.t1:0.07554,(EmaiTE_00001962_INT#LTR/Gypsy.g663.t1:0.06553,EmaiTE_00002526_INT#LTR/Gypsy.g988.t1:0.08168)0.431:0.02514)0.774:0.02504,EmaiTE_00002190_INT#LTR/Gypsy.g806.t1:0.20785)0.309:0.00054)0.812:0.04575)0.865:0.04029,((EmusTE_00002195_INT#LTR/Gypsy.g529.t1:0.05720,(EmusTE_00001140_INT#LTR/Gypsy.g211.t1:0.08462,EmusTE_00001401_INT#LTR/Gypsy.g296.t1:0.02442)0.796:0.05347)0.997:0.24939,(EmaiTE_00003026_INT#LTR/Gypsy.g1248.t1:0.14329,(EmaiTE_00002367_INT#LTR/Gypsy.g900.t1:0.04448,(EmaiTE_00001179_INT#LTR/Gypsy.g227.t1:0.03315,EmaiTE_00001056_INT#LTR/Gypsy.g172.t1:0.04395)0.747:0.00998)0.975:0.10761)0.613:0.03393)0.554:0.05748)0.748:0.02181,(EmaiTE_00002619_INT#LTR/Gypsy.g1049.t1:0.13577,((EmaiTE_00003145_INT#LTR/Gypsy.g1306.t1:0.09769,EmaiTE_00001891_INT#LTR/Gypsy.g626.t1:0.07336)0.985:0.08898,(EmaiTE_00000941_INT#LTR/Gypsy.g111.t1:0.09566,EmaiTE_00003194_INT#LTR/Gypsy.g1341.t1:0.05634)0.000:0.00050)0.923:0.06574)0.779:0.02399)0.987:0.13764)0.250:0.03382)0.694:0.01637,(EmaiTE_00002424_INT#LTR/Gypsy.g940.t1:0.38777,((EmusTE_00000523_INT#LTR/Gypsy.g21.t1:0.13981,EmusTE_00001082_INT#LTR/Gypsy.g191.t1:0.23190)0.726:0.03133,(((zradTE_00001145_INT#LTR/Gypsy.g230.t1:0.15548,zradTE_00001149_INT#LTR/Gypsy.g235.t1:0.10154)0.914:0.11208,(zradTE_00001195_INT#LTR/Gypsy.g256.t1:0.25554,((zradTE_00000726_INT#LTR/Gypsy.g28.t1:0.00077,EmaiTE_00001378_INT#LTR/Gypsy.g343.t1:0.61276)0.131:0.13242,(zradTE_00001018_INT#LTR/Gypsy.g173.t1:0.11064,zradTE_00000730_INT#LTR/Gypsy.g31.t1:0.07189)0.854:0.05702)0.806:0.04865)0.891:0.05560)0.078:0.00319,EmaiTE_00002120_INT#LTR/Gypsy.g763.t1:0.35860)0.231:0.03861)0.800:0.03141)0.775:0.02175)0.663:0.01445)0.919:0.06664,EmaiTE_00002935_INT#LTR/Gypsy.g1191.t1:0.11925)0.665:0.00715,((((McicTE_00001382_INT#LTR/Gypsy.g62.t1:0.13740,McicTE_00001596_INT#LTR/Gypsy.g85.t1:0.09859)0.812:0.04964,(zradTE_00000985_INT#LTR/Gypsy.g163.t1:0.63971,(EmusTE_00001915_INT#LTR/Gypsy.g439.t1:0.12972,EmaiTE_00001907_INT#LTR/Gypsy.g635.t1:0.19497)0.909:0.12569)0.058:0.04699)0.755:0.03181,EmusTE_00001392_INT#LTR/Gypsy.g293.t1:0.08136)0.719:0.01630,zradTE_00000745_INT#LTR/Gypsy.g43.t1:0.24856)0.851:0.03849)0.728:0.00200)0.434:0.01436);

## sharon_TE_tree_Example.Rproj
Version: 1.0

RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default

EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8

RnwWeave: Sweave
LaTeX: pdfLaTeX

## tree_percentage.pdf

      
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## tree_percentage_gg.pdf

      
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	#!/usr/bin/env R
	library(ggtree)
	library(dplyr)
	library(tidyverse)
	library(treedataverse)
	library(ape)
	tree<-read.tree("RVT_1matching_sequences.tree")
	labelfix <- tibble(label = tree$tip.label) %>%
	mutate(label2 = str_replace(label,'#\\S+',''),
	species = str_replace(label,"_\\S+$",""))

	tree <- full_join(tree, labelfix, by = "label") %>%
	mutate(old_label = label, label = label2)

	fams1 <- read_tsv("RVT1_fams.tsv",col_types ='fid')
	#fams <- read.table("RVT1_fams.tsv", sep="\t", stringsAsFactor=F)
	#fams1 is the table I want to attach `x`

	g1 <- ggplot(tree, aes(x, y)) + geom_tree() +
	geom_tiplab(aes(label = label, color=species),
	size=1,linesize=.5) + theme_tree() +
	scale_colour_brewer(palette = "Dark2")

	g1

	p <- g1 + geom_facet(panel = "Percentages",
	data = fams1, geom = geom_col,
	aes(x = percentage), orientation = 'y', width = 0.8) +
	theme_tree2()
	pdf("tree_percentage.pdf")
	p
	ggsave("tree_percentage_gg.pdf",p,height=10)

	#gheatmap(g1, fams, offset=8, width=1,
	# colnames=FALSE, legend_title="TE family") +
	# scale_x_ggtree() +
	# scale_y_continuous(expand=c(0, 0.3))
family	n	percentage
EmaiTE_00001583_INT	4606	1.2098658124698642
EmaiTE_00003084_INT	3953	1.180466728466515
EmaiTE_00002448_INT	3729	1.1046748952813175
EmaiTE_00002736_INT	7645	0.843423229290474
EmaiTE_00002120_INT	4851	0.7875355040374232
EmaiTE_00002179_INT	2019	0.7257274308207773
EmaiTE_00003215_INT	2334	0.6388513420942799
EmaiTE_00001907_INT	1196	0.5869870555039892
EmaiTE_00002798_INT	2035	0.5764564997407257
EmaiTE_00002371_INT	2948	0.500422242717028
EmaiTE_00003098_INT	1272	0.42289952537117886
EmaiTE_00002725_INT	1961	0.3562131281683175
EmaiTE_00001450_INT	2227	0.3424198985828054
EmaiTE_00002326_INT	972	0.32717009092882343
EmaiTE_00001777_INT	2617	0.2768087643026514
EmaiTE_00002053_INT	1198	0.27236831254519245
EmaiTE_00003159_INT	1045	0.2601018698208323
EmaiTE_00000941_INT	855	0.2502278680210197
EmaiTE_00001387_INT	1853	0.2431909628327413
EmaiTE_00000912_INT	2047	0.2309463967611734
EmaiTE_00001159_INT	618	0.2301875821649028
EmaiTE_00001305_INT	364	0.22853708198427836
EmaiTE_00001392_INT	699	0.21672004336766598
EmaiTE_00000821_INT	660	0.18643385261426826
EmaiTE_00002626_INT	534	0.18384443702136263
EmaiTE_00002322_INT	1579	0.1833572151339818
EmaiTE_00001179_INT	402	0.18069954099263522
EmaiTE_00002939_INT	752	0.1753017736924457
EmaiTE_00000891_INT	322	0.16857707716921014
EmaiTE_00000781_INT	1583	0.162805626113767
EmaiTE_00001882_INT	771	0.15969006854188503
EmaiTE_00003145_INT	332	0.1507198777580126
EmaiTE_00002653_INT	430	0.14196209400997192
EmaiTE_00002619_INT	383	0.12847157624798047
EmaiTE_00002348_INT	885	0.12787743010024682
EmaiTE_00002922_INT	420	0.12696318951727778
EmaiTE_00003026_INT	356	0.12446407871206108
EmaiTE_00000878_INT	523	0.11836939587195108
EmaiTE_00001935_INT	401	0.11787445780083346
EmaiTE_00003029_INT	554	0.11680529999053325
EmaiTE_00002833_INT	535	0.11488363106715843
EmaiTE_00001091_INT	442	0.11035575749175831
EmaiTE_00001058_INT	1948	0.10985810603734864
EmaiTE_00002170_INT	321	0.10556053086886227
EmaiTE_00002185_INT	574	0.10305785874807472
EmaiTE_00001466_INT	356	0.09085026252386118
EmaiTE_00003170_INT	715	0.0881790214660543
EmaiTE_00002850_INT	305	0.08624726214856213
EmaiTE_00002935_INT	244	0.0850848317875973
EmaiTE_00001631_INT	641	0.0815220747318924
EmaiTE_00002255_INT	936	0.0789074755503073
EmaiTE_00003201_INT	425	0.07778142148410169
EmaiTE_00002346_INT	318	0.07394300164456889
EmaiTE_00001720_INT	234	0.07280092165829455
EmaiTE_00001056_INT	392	0.0716264506589712
EmaiTE_00002698_INT	724	0.06424308034158766
EmaiTE_00003149_INT	652	0.06134518698566574
EmaiTE_00002940_INT	784	0.06101805471251655
EmaiTE_00002544_INT	228	0.0574697972987786
EmaiTE_00001501_INT	350	0.05446743868611232
EmaiTE_00002190_INT	737	0.05441028805052326
EmaiTE_00000846_INT	1018	0.053189604742007006
EmaiTE_00001968_INT	192	0.052443593923145786
EmaiTE_00001891_INT	214	0.05126216987913654
EmaiTE_00002269_INT	574	0.04458801011971561
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