A package for the mass calculation and visualisation of reference plasmid coverage within whole genome sequence datasets.
This package was built based off a script produced for a previous publication. If you use plasmid_mapR please cite the following paper:
Cummins, Max L., et al. "Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene." Microbial genomics 5.2 (2019).
# Install devtools
install.packages("devtools")
# Load devtools
library(devtools)
#Download plasmidmapR
install_github("maxlcummins/plasmidmapR")
#Load plasmidmapR
library(plasmidmapR)
Basic usage:
plasmidmapR(path_to_abricate,
plasmid_reference_name,
output_directory,
min_hit_id = 90,
min_hit_length = 0.5,
writecsv = FALSE,
path_to_tree = FALSE,
tree_reference_name = "Placeholder")
Input data should be generated using abricate version 0.9.8
Note that version 1.0 doesn't work and will produce only blank output files.
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggtree_2.2.4 tidytree_0.3.3 reshape2_1.4.4 magrittr_2.0.1 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.5
[8] purrr_0.3.4 readr_1.3.1 tidyr_1.1.1 tibble_3.1.0 tidyverse_1.3.0 ggplot2_3.3.2 pheatmap_1.0.12
[15] plasmidmapR_0.1.0
loaded via a namespace (and not attached):
[1] treeio_1.12.0 tidyselect_1.1.0 lattice_0.20-41 haven_2.3.1 colorspace_1.4-1 vctrs_0.3.7
[7] generics_0.1.0 utf8_1.2.1 blob_1.2.1 rlang_0.4.10 pillar_1.5.1 glue_1.4.2
[13] withr_2.2.0 DBI_1.1.0 dbplyr_1.4.4 RColorBrewer_1.1-2 modelr_0.1.8 readxl_1.3.1
[19] rvcheck_0.1.8 lifecycle_1.0.0 plyr_1.8.6 munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0
[25] rvest_0.3.6 parallel_4.0.2 fansi_0.4.2 broom_0.7.0 Rcpp_1.0.6 BiocManager_1.30.10
[31] backports_1.1.9 scales_1.1.1 jsonlite_1.7.2 fs_1.5.0 aplot_0.0.5 hms_1.0.0
[37] stringi_1.5.3 grid_4.0.2 cli_2.4.0 tools_4.0.2 patchwork_1.0.1 lazyeval_0.2.2
[43] ape_5.4-1 crayon_1.4.1 pkgconfig_2.0.3 ellipsis_0.3.1 xml2_1.3.2 reprex_0.3.0
[49] lubridate_1.7.9 assertthat_0.2.1 httr_1.4.2 rstudioapi_0.11 R6_2.5.0 nlme_3.1-149
[55] compiler_4.0.2