Last updated: 2020-09-18
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Knit directory: R_gene_analysis/
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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(knitr)Here i make some of the tables for the manuscript.
files_to_make_tables_for <- list.files(path = './data', pattern = '*lst')
files_to_make_tables_for[1] "Lee.NBS.candidates.lst" "Lee.preRGA.candidates.by.Blast.lst"
[3] "Lee.RGA.candidates.lst" "Lee.RLK.candidates.lst"
[5] "Lee.RLP.candidates.lst" "Lee.TMCC.candidates.lst" The following will print warnings because I assume 3 columns, but some files have only 2:
[1] “Lee.NBS.candidates.lst”| Var1 | Freq |
|---|---|
| CN | 13 |
| CNL | 123 |
| NBS | 52 |
| NL | 95 |
| OTHER | 20 |
| TN | 22 |
| TNL | 99 |
| TX | 62 |
| Var1 | Freq |
|---|---|
| NA | 14358 |
| Var1 | Freq |
|---|---|
| CN | 13 |
| CNL | 123 |
| NBS | 52 |
| NL | 95 |
| OTHER | 20 |
| RLK | 1173 |
| RLP | 180 |
| TM-CC | 280 |
| TN | 22 |
| TNL | 99 |
| TX | 62 |
| Var1 | Freq |
|---|---|
| RLK_lrr | 470 |
| RLK_lysm | 19 |
| RLK_other_receptor | 684 |
| Var1 | Freq |
|---|---|
| RLP_lrr | 177 |
| RLP_lysm | 3 |
| Var1 | Freq |
|---|---|
| TM-CC | 280 |
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] knitr_1.29 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.0
[5] purrr_0.3.4 readr_1.3.1 tidyr_1.1.0 tibble_3.0.2
[9] ggplot2_3.3.2 tidyverse_1.3.0
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.15 haven_2.3.1 lattice_0.20-41
[5] colorspace_1.4-1 vctrs_0.3.1 generics_0.0.2 htmltools_0.5.0
[9] yaml_2.2.1 blob_1.2.1 rlang_0.4.6 later_1.1.0.1
[13] pillar_1.4.4 withr_2.2.0 glue_1.4.1 DBI_1.1.0
[17] dbplyr_1.4.4 modelr_0.1.8 readxl_1.3.1 lifecycle_0.2.0
[21] munsell_0.5.0 gtable_0.3.0 workflowr_1.6.2 cellranger_1.1.0
[25] rvest_0.3.5 evaluate_0.14 httpuv_1.5.4 fansi_0.4.1
[29] highr_0.8 broom_0.5.6 Rcpp_1.0.5 promises_1.1.1
[33] backports_1.1.8 scales_1.1.1 jsonlite_1.7.0 fs_1.5.0.9000
[37] hms_0.5.3 digest_0.6.25 stringi_1.4.6 grid_3.6.3
[41] rprojroot_1.3-2 cli_2.0.2 tools_3.6.3 magrittr_1.5
[45] crayon_1.3.4 pkgconfig_2.0.3 ellipsis_0.3.1 xml2_1.3.2
[49] reprex_0.3.0 lubridate_1.7.9 assertthat_0.2.1 rmarkdown_2.3
[53] httr_1.4.1 rstudioapi_0.11 R6_2.4.1 nlme_3.1-148
[57] git2r_0.26.1 compiler_3.6.3