Genomic comparison
Philipp Bayer
4 March 2021
Last updated: 2021-10-07
Checks: 7 0
Knit directory: Amphibolis_Posidonia_Comparison/
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library(tidyverse)-- Attaching packages --------------------------------------- tidyverse 1.3.1 --v ggplot2 3.3.5 v purrr 0.3.4
v tibble 3.1.5 v dplyr 1.0.7
v tidyr 1.1.4 v stringr 1.4.0
v readr 2.0.2 v forcats 0.5.1-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()library(cowplot)
theme_set(theme_cowplot())
library(RColorBrewer)
library(wesanderson)
library(patchwork)
Attaching package: 'patchwork'The following object is masked from 'package:cowplot':
align_plots# reps <- data.frame(
# stringsAsFactors = FALSE,
# Class = c("LINEs","LTRs","DNA",
# "Unclassified","Non-repetitive","LINEs","LTRs","DNA","Unclassified",
# "Non-repetitive","LINEs","LTRs","DNA","Unclassified",
# "Non-repetitive","LINEs","LTRs","DNA","Unclassified","Non-repetitive"),
# Assembly = c("A. antarctica","A. antarctica",
# "A. antarctica","A. antarctica","A. antarctica","P. australis",
# "P. australis","P. australis","P. australis","P. australis","Z. marina",
# "Z. marina","Z. marina","Z. marina","Z. marina","Z. muelleri",
# "Z. muelleri","Z. muelleri","Z. muelleri","Z. muelleri"),
# BP = c(805898L,45776664L,37822890L,
# 1546483L,158725395L,38319733L,611240734L,100034681L,
# 37142931L,428369702L,3103364L,123623579L,27390818L,
# 6060480L,96439714L,14331182L,164253396L,142828758L,
# 21922574L,274954485L),
# Percent = c(0.33,18.71,15.46,0.63,
# 64.87131,3.15,50.3,8.23,3.06,35.25364,1.19,47.46,10.52,
# 2.33,37.02,2.32,26.57,23.1,3.55,44.46)
# )
reps <- readxl::read_xlsx('./data/Repeat_coding.xlsx')
reps <- reps %>% dplyr::filter(Class != 'Total')
reps$Class <- factor(reps$Class, levels = c('LINEs', 'LTRs', 'DNA', 'Unclassified', 'Total CDS', 'Non-repetitive'))
reps# A tibble: 24 x 4
Class Assembly BP Percent
<fct> <chr> <dbl> <dbl>
1 LINEs A. antarctica 805898 0.329
2 LTRs A. antarctica 45776664 18.7
3 DNA A. antarctica 37822890 15.5
4 Unclassified A. antarctica 1546483 0.632
5 Total CDS A. antarctica 29544393 12.1
6 Non-repetitive A. antarctica 129181002 52.8
7 LINEs P. australis 38319733 3.15
8 LTRs P. australis 611240734 50.3
9 DNA P. australis 100034681 8.23
10 Unclassified P. australis 37142931 3.06
# ... with 14 more rowspal <- wes_palette("Zissou1", 6, type = "continuous")
p1 <- reps %>% ggplot(aes(x=Assembly, fill=Class, y = BP/1000000)) +
geom_bar(position='stack', stat='identity') + ylab('Size (Mbp)') +
#scale_fill_brewer(palette='Dark2') +
scale_fill_manual(values=pal) +
theme(axis.text.x = element_text(face="italic"))
p1
p2 <- reps %>% ggplot(aes(x=Assembly, fill=Class, y = Percent)) + geom_bar(position='stack', stat='identity')+
#scale_fill_brewer(palette='Dark2') +
scale_fill_manual(values=pal) +
theme(axis.text.x = element_text(face="italic")) +
ylab('Percent\n of assembly')
p2
patch <- p1/p2 + plot_annotation(tag_levels = 'A')
patch[[1]] = patch[[1]] + theme(axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.x = element_blank() )
patch
reps %>% filter(Class=='Non-repetitive') %>% ggplot(aes(x=Assembly, fill=Class, y = BP)) + geom_bar(position='stack', stat='identity')
sessionInfo()R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_1.1.1 wesanderson_0.3.6 RColorBrewer_1.1-2 cowplot_1.1.1
[5] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[9] readr_2.0.2 tidyr_1.1.4 tibble_3.1.5 ggplot2_3.3.5
[13] tidyverse_1.3.1 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 lubridate_1.7.10 assertthat_0.2.1 rprojroot_2.0.2
[5] digest_0.6.28 utf8_1.2.2 R6_2.5.1 cellranger_1.1.0
[9] backports_1.2.1 reprex_2.0.1 evaluate_0.14 highr_0.9
[13] httr_1.4.2 pillar_1.6.3 rlang_0.4.11 readxl_1.3.1
[17] rstudioapi_0.13 whisker_0.4 jquerylib_0.1.4 rmarkdown_2.11
[21] labeling_0.4.2 munsell_0.5.0 broom_0.7.9 compiler_4.1.1
[25] httpuv_1.6.3 modelr_0.1.8 xfun_0.26 pkgconfig_2.0.3
[29] htmltools_0.5.2 tidyselect_1.1.1 fansi_0.5.0 crayon_1.4.1
[33] tzdb_0.1.2 dbplyr_2.1.1 withr_2.4.2 later_1.3.0
[37] grid_4.1.1 jsonlite_1.7.2 gtable_0.3.0 lifecycle_1.0.1
[41] DBI_1.1.1 git2r_0.28.0 magrittr_2.0.1 scales_1.1.1
[45] cli_3.0.1 stringi_1.7.5 farver_2.1.0 fs_1.5.0
[49] promises_1.2.0.1 xml2_1.3.2 ellipsis_0.3.2 generics_0.1.0
[53] vctrs_0.3.8 tools_4.1.1 glue_1.4.2 hms_1.1.1
[57] fastmap_1.1.0 yaml_2.2.1 colorspace_2.0-2 rvest_1.0.1
[61] knitr_1.36 haven_2.4.3