## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("fobitools") ## ----warning = FALSE, message = FALSE, comment = FALSE------------------------ library(fobitools) ## ----warning = FALSE, message = FALSE, comment = FALSE------------------------ library(tidyverse) library(kableExtra) ## ----warning = FALSE, message = FALSE, comment = FALSE------------------------ load("data/sample_ffq.rda") sample_ffq %>% dplyr::slice(1L:10L) %>% kbl(row.names = FALSE, booktabs = TRUE) %>% kable_styling(latex_options = c("striped")) ## ----warning = FALSE---------------------------------------------------------- annotated_text <- fobitools::annotate_foods(sample_ffq) annotated_text$annotated %>% dplyr::slice(1L:10L) %>% kbl(row.names = FALSE, booktabs = TRUE) %>% kable_styling(latex_options = c("striped")) ## ----warning = FALSE---------------------------------------------------------- annotated_text_95 <- fobitools::annotate_foods(sample_ffq, similarity = 0.95) annotated_text_95$annotated %>% dplyr::slice(1L:10L) %>% kbl(row.names = FALSE, booktabs = TRUE) %>% kable_styling(latex_options = c("striped")) ## ----warning = FALSE---------------------------------------------------------- annotated_text$annotated %>% filter(!FOOD_ID %in% annotated_text_95$annotated$FOOD_ID) %>% kbl(row.names = FALSE, booktabs = TRUE) %>% kable_styling(latex_options = c("striped")) ## ----warning = FALSE, message = FALSE, comment = FALSE, fig.width = 12, fig.height = 10---- terms <- annotated_text$annotated %>% pull(FOBI_ID) fobitools::fobi_graph(terms = terms, get = NULL, layout = "lgl", labels = TRUE, legend = TRUE, labelsize = 6, legendSize = 20) ## ----warning = FALSE---------------------------------------------------------- inverse_rel <- fobitools::fobi %>% filter(id_BiomarkerOf %in% annotated_text$annotated$FOBI_ID) %>% dplyr::select(id_code, name, id_BiomarkerOf, FOBI) %>% dplyr::rename(METABOLITE_ID = 1, METABOLITE_NAME = 2, FOBI_ID = 3, METABOLITE_FOBI_ID = 4) annotated_foods_and_metabolites <- left_join(annotated_text$annotated, inverse_rel, by = "FOBI_ID") annotated_foods_and_metabolites %>% filter(!is.na(METABOLITE_ID)) %>% dplyr::slice(1L:10L) %>% kbl(row.names = FALSE, booktabs = TRUE) %>% kable_styling(latex_options = c("striped")) ## ----------------------------------------------------------------------------- sessionInfo()