Last updated: 2022-01-18
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Knit directory: HenriqueDGen/
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Descriptive and deviance analysis were performed to verify the distribution and the genotypic effects for resistance to foliar diseases. In this work we used a natural logarithm transformation for Affected area by Anthracnosis at the innoculated area at stem in cassava plants (AnAr).
suppressMessages(library(tidyverse))
library(here)here() starts at /Users/lbd54/Documents/GitHub/HenriqueDGensuppressMessages(library(reactable))
# Data read by R using here package to allow the read in any computer with different directory path
PhenoData <- readRDS(here::here("data", "DadosFenotipicos.RDS"))
# Add the control information for the Mixed Models analysis
control <- names(table(PhenoData$accession_name)[table(PhenoData$accession_name) > 30])
PhenoData$control <- ifelse(PhenoData$accession_name %in% control, PhenoData$accession_name, "999")
PhenoData$new <- ifelse(PhenoData$accession_name %in% control, 0, 1)
# Change the Disease names to english abbreviations
colnames(PhenoData)[7:11] <- c("Anth", "WhLS", "BrLS", "BlLS", "AnAr")
# Natural logarithm transformation for Anthracnosis Area
PhenoData$AnAr <- log(PhenoData$AnAr)Anthracnosis (Anth), White Leaf spot (WhLS), Brown Leaf spot (BrLS), Blight Leaf Spot (BlLS), Affected area by Anthracnosis at the innoculated area at stem in cassava plants (AnAr).
lnfUtl <- colnames(PhenoData)[c(1:4, 12:13)]
PhenoData$talhao_number <- NULL
PhenoData$Idade <- NULL
traits <- colnames(PhenoData)[!colnames(PhenoData) %in% lnfUtl]
PhenoData2 <- PhenoData %>% gather(key = traits, value = Y, -all_of(lnfUtl))Anthracnosis (Anth), White Leaf spot (WhLS), Brown Leaf spot (BrLS), Blight Leaf Spot (BlLS), Affected area by Anthracnosis at the innoculated area at stem in cassava plants (AnAr).
saveRDS(PhenoData2, here::here("output", "DadosFenotipicosv2.RDS"))| Característica | Sigla |
|---|---|
| Genotipos - 1˚coluna | Genotipos.BGM |
| Altura.de.planta….CO_334.0000018 | AP |
| Altura.de.planta.sem.folha….CO_334.0000125 | APsF |
| PTR - Produtividade Total de Raizes | PTR |
| PRC - Produtividade de Raiz Comercial | PRC |
| PRNC - Produtividade de Raizes ñ comerciais | PRNC |
| Peso.da.parte.aerea….CO_334.0000016 | PPA |
| Vigor.Inicial | Vigor |
| Vigor.da.planta.45.DAP..1-5. | Vigor45D |
| Vigor.da.planta.6.MAP..1-5. | Vigor6M |
| Vigor.da.planta.12.MAP..1-5. | Vigor12M |
colnames(DadosPhen)[c(18, 12, 13, 20)] <- c("PortePl","AltPl", "AltPlsF",
"Vigor", "PPA")separar a característica Vigor em outro objeto do R, sem perder as informações de:
Transformar as várias colunas do objeto com as informações de Vigor em uma única coluna, e adicionar uma coluna com o número da amostra de avaliação de Vigor.
RawPhenoData %>% mutate("FlowerPresence" = flower.visual.rating.0.1.CO_334.0000111,
"FlowerVisRate" = flowering.ability.visual.assessment.0.3.CO_334.0000233,
.keep = "unused") %>% melt(data = .,
id.vars = c("studyYear", "locationName", "germplasmName",
"replicate", "blockNumber", "plotNumber",
"plantNumber"),
variable.name = "Trait",
value.name = "Value") -> PhenoData# Rodar o script aqui dentro
sessionInfo()R version 4.1.1 (2021-08-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.6.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reactable_0.2.3 here_1.0.1 forcats_0.5.1 stringr_1.4.0
[5] dplyr_1.0.7 purrr_0.3.4 readr_2.1.1 tidyr_1.1.4
[9] tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 lubridate_1.8.0 assertthat_0.2.1 rprojroot_2.0.2
[5] digest_0.6.29 utf8_1.2.2 reactR_0.4.4 R6_2.5.1
[9] cellranger_1.1.0 backports_1.4.1 reprex_2.0.1 evaluate_0.14
[13] httr_1.4.2 pillar_1.6.4 rlang_0.4.12 readxl_1.3.1
[17] rstudioapi_0.13 whisker_0.4 jquerylib_0.1.4 rmarkdown_2.11
[21] htmlwidgets_1.5.4 munsell_0.5.0 broom_0.7.11 compiler_4.1.1
[25] httpuv_1.6.5 modelr_0.1.8 xfun_0.29 pkgconfig_2.0.3
[29] htmltools_0.5.2 tidyselect_1.1.1 workflowr_1.7.0 fansi_1.0.0
[33] crayon_1.4.2 tzdb_0.2.0 dbplyr_2.1.1 withr_2.4.3
[37] later_1.3.0 grid_4.1.1 jsonlite_1.7.2 gtable_0.3.0
[41] lifecycle_1.0.1 DBI_1.1.2 git2r_0.29.0 magrittr_2.0.1
[45] scales_1.1.1 cli_3.1.0 stringi_1.7.6 fs_1.5.2
[49] promises_1.2.0.1 xml2_1.3.3 bslib_0.3.1 ellipsis_0.3.2
[53] generics_0.1.1 vctrs_0.3.8 tools_4.1.1 glue_1.6.0
[57] crosstalk_1.2.0 hms_1.1.1 fastmap_1.1.0 yaml_2.2.1
[61] colorspace_2.0-2 rvest_1.0.2 knitr_1.37 haven_2.4.3
[65] sass_0.4.0