Untitled
Philipp Bayer
4 March 2021
Last updated: 2021-04-14
Checks: 7 0
Knit directory: Amphibolis_Posidonia_Comparison/
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library(tidyverse)-- Attaching packages ------------------------------------------------------------------------------------------------------------------- tidyverse 1.3.0 --v ggplot2 3.3.2 v purrr 0.3.4
v tibble 3.0.2 v dplyr 1.0.0
v tidyr 1.1.0 v stringr 1.4.0
v readr 1.3.1 v forcats 0.5.0-- Conflicts ---------------------------------------------------------------------------------------------------------------------- tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()library(cowplot)
********************************************************Note: As of version 1.0.0, cowplot does not change the default ggplot2 theme anymore. To recover the previous behavior, execute:
theme_set(theme_cowplot())********************************************************theme_set(theme_cowplot())
library(RColorBrewer)
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 rowsp1 <- reps %>% ggplot(aes(x=Assembly, fill=Class, y = BP/1000000)) +
geom_bar(position='stack', stat='identity') + ylab('Size (Mbp)') +
scale_fill_brewer(palette='Dark2') +
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') +
theme(axis.text.x = element_text(face="italic")) +
ylab('Percent\n of assembly')
p2
p1/p2 + plot_annotation(tag_levels = 'A')
reps %>% filter(Class=='Non-repetitive') %>% ggplot(aes(x=Assembly, fill=Class, y = BP)) + geom_bar(position='stack', stat='identity')
sessionInfo()R version 3.6.3 (2020-02-29)
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_1.0.0 RColorBrewer_1.1-2 cowplot_1.0.0
[4] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.0
[7] purrr_0.3.4 readr_1.3.1 tidyr_1.1.0
[10] tibble_3.0.2 ggplot2_3.3.2 tidyverse_1.3.0
[13] workflowr_1.6.2.9000
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 lubridate_1.7.9 lattice_0.20-41 getPass_0.2-2
[5] ps_1.3.4 utf8_1.1.4 assertthat_0.2.1 rprojroot_1.3-2
[9] digest_0.6.25 R6_2.4.1 cellranger_1.1.0 backports_1.1.10
[13] reprex_0.3.0 evaluate_0.14 httr_1.4.2 pillar_1.4.4
[17] rlang_0.4.7 readxl_1.3.1 rstudioapi_0.11 whisker_0.4
[21] callr_3.4.4 blob_1.2.1 rmarkdown_2.3 labeling_0.3
[25] munsell_0.5.0 broom_0.5.6 compiler_3.6.3 httpuv_1.5.4
[29] modelr_0.1.8 xfun_0.17 pkgconfig_2.0.3 htmltools_0.5.0
[33] tidyselect_1.1.0 fansi_0.4.1 crayon_1.3.4 dbplyr_1.4.4
[37] withr_2.2.0 later_1.1.0.1 grid_3.6.3 nlme_3.1-148
[41] jsonlite_1.7.1 gtable_0.3.0 lifecycle_0.2.0 DBI_1.1.0
[45] git2r_0.27.1 magrittr_1.5 scales_1.1.1 cli_2.0.2
[49] stringi_1.5.3 farver_2.0.3 fs_1.5.0.9000 promises_1.1.1
[53] xml2_1.3.2 ellipsis_0.3.1 generics_0.0.2 vctrs_0.3.1
[57] tools_3.6.3 glue_1.4.2 hms_0.5.3 processx_3.4.4
[61] yaml_2.2.1 colorspace_1.4-1 rvest_0.3.5 knitr_1.29
[65] haven_2.3.1