Last updated: 2020-12-11
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Knit directory: R_gene_analysis/
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|---|---|---|---|---|
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| html | dae157b | Philipp Bayer | 2020-09-24 | Update of analysis |
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| html | 0777e1d | Philipp Bayer | 2020-09-22 | update |
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| Rmd | c71005a | Philipp Bayer | 2020-09-18 | lots changes |
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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" Let’s print the counts of R-gene classes for each type, that will be table 1:
for(i in seq_along(files_to_make_tables_for)) {
f <- files_to_make_tables_for[i]
fh <- read_tsv(paste('./data/', f, sep=''), col_names = c('Name','Class','Type'))
fh <- fh %>% unite(United, Class, Type)
# remove NAs in files with 2 columns
fh$United <- gsub(pattern = '_NA', replacement = '', fh$United)
# now split into pangenome genes and reference genome genes
pan_fh <- fh %>% filter(str_detect(Name, 'UWA'))
ref_fh <- fh %>% filter(!str_detect(Name, 'UWA'))
print(f)
print(kable(table(fh$United), 'html'))
print('Reference')
print(kable(table(ref_fh$United), 'html'))
print('Pangenome')
print(kable(table(pan_fh$United), 'html'))
}| Var1 | Freq |
|---|---|
| CN | 13 |
| CNL | 123 |
| NBS | 52 |
| NL | 95 |
| OTHER | 20 |
| TN | 22 |
| TNL | 99 |
| TX | 62 |
| Var1 | Freq |
|---|---|
| CN | 8 |
| CNL | 123 |
| NBS | 29 |
| NL | 92 |
| OTHER | 20 |
| TN | 22 |
| TNL | 99 |
| TX | 49 |
| Var1 | Freq |
|---|---|
| CN | 5 |
| NBS | 23 |
| NL | 3 |
| TX | 13 |
| Var1 | Freq |
|---|---|
| NA | 14358 |
| Var1 | Freq |
|---|---|
| NA | 13448 |
| Var1 | Freq |
|---|---|
| NA | 910 |
| 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 |
|---|---|
| CN | 8 |
| CNL | 123 |
| NBS | 29 |
| NL | 92 |
| OTHER | 20 |
| RLK | 1164 |
| RLP | 170 |
| TM-CC | 273 |
| TN | 22 |
| TNL | 99 |
| TX | 49 |
| Var1 | Freq |
|---|---|
| CN | 5 |
| NBS | 23 |
| NL | 3 |
| RLK | 9 |
| RLP | 10 |
| TM-CC | 7 |
| TX | 13 |
| Var1 | Freq |
|---|---|
| RLK_lrr | 470 |
| RLK_lysm | 19 |
| RLK_other_receptor | 684 |
| Var1 | Freq |
|---|---|
| RLK_lrr | 469 |
| RLK_lysm | 19 |
| RLK_other_receptor | 676 |
| Var1 | Freq |
|---|---|
| RLK_lrr | 1 |
| RLK_other_receptor | 8 |
| Var1 | Freq |
|---|---|
| RLP_lrr | 177 |
| RLP_lysm | 3 |
| Var1 | Freq |
|---|---|
| RLP_lrr | 167 |
| RLP_lysm | 3 |
| Var1 | Freq |
|---|---|
| RLP_lrr | 10 |
| Var1 | Freq |
|---|---|
| TM-CC | 280 |
| Var1 | Freq |
|---|---|
| TM-CC | 273 |
| Var1 | Freq |
|---|---|
| TM-CC | 7 |
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
[4] dplyr_1.0.0 purrr_0.3.4 readr_1.3.1
[7] tidyr_1.1.0 tibble_3.0.2 ggplot2_3.3.2
[10] tidyverse_1.3.0 workflowr_1.6.2.9000
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.17 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_0.4.7 later_1.1.0.1
[13] pillar_1.4.4 withr_2.2.0 glue_1.4.2 DBI_1.1.0
[17] dbplyr_1.4.4 readxl_1.3.1 modelr_0.1.8 lifecycle_0.2.0
[21] cellranger_1.1.0 munsell_0.5.0 gtable_0.3.0 rvest_0.3.5
[25] evaluate_0.14 callr_3.4.4 httpuv_1.5.4 ps_1.3.4
[29] fansi_0.4.1 highr_0.8 broom_0.5.6 Rcpp_1.0.5
[33] promises_1.1.1 backports_1.1.10 scales_1.1.1 jsonlite_1.7.1
[37] fs_1.5.0.9000 hms_0.5.3 digest_0.6.25 stringi_1.5.3
[41] processx_3.4.4 getPass_0.2-2 rprojroot_1.3-2 grid_3.6.3
[45] cli_2.0.2 tools_3.6.3 magrittr_1.5 crayon_1.3.4
[49] whisker_0.4 pkgconfig_2.0.3 ellipsis_0.3.1 xml2_1.3.2
[53] reprex_0.3.0 lubridate_1.7.9 assertthat_0.2.1 rmarkdown_2.3
[57] httr_1.4.2 rstudioapi_0.11 R6_2.4.1 nlme_3.1-148
[61] git2r_0.27.1 compiler_3.6.3