diff --git a/global.R b/global.R index 61fd637..7800e2e 100644 --- a/global.R +++ b/global.R @@ -39,7 +39,8 @@ tAntibiotics = readxl::read_xlsx('data/ab_mapping.xlsx') %>% # radar_data <- readGlimsArchive(ymdStartDate = ymdStartDate, # ymdEndDate = ymdEndDate, # readPreprocessed = T) -radar_data <- readGlimsFinalResults() +radar_data <- readGlimsFinalResults() %>% + mutate_if(is.rsi, as.sir) if (!'CRO' %in% colnames(radar_data)) radar_data <- radar_data %>% add_column('CRO' = '') @@ -85,7 +86,7 @@ suppressMessages( ) intrinsic_info <- AMR::intrinsic_resistant %>% - mutate(mo = as.mo(microorganism), + mutate(#mo = as.mo(microorganism), intrinsic_r = TRUE) diff --git a/server.R b/server.R index 4cece77..fd83780 100644 --- a/server.R +++ b/server.R @@ -696,13 +696,28 @@ server <- function(input, output, session) { "Vancomycin") get_resistance_df <- function(.data, mo_selected, abx, language = "en") { - .data %>% - filter(mo == as.mo(mo_selected)) %>% - {if (nrow(.) != 0) { - group_by_at(., input$box1.2_group) %>% - select(group_vars(.), as.character(as.ab(abx))) %>% - count_df(., translate_ab = "name", language = language) - }} + + out <- .data %>% + filter(mo == as.mo(mo_selected)) + + print(paste("rijen voor ", mo_selected, ":", nrow(out))) + abx <- gsub("Co-trimoxazole", "Trimetoprim / sufamethoxazole", abx) + + if (nrow(out) > 0) { + out %>% + select(mo, as.character(as.ab(abx))) %>% + count_df(., translate_ab = "name", language = language) + } else { + out + } + + # .data %>% + # filter(mo == as.mo(mo_selected)) %>% + # {if (nrow(.) != 0) { + # group_by_at(., input$box1.2_group) %>% + # select(group_vars(.), as.character(as.ab(abx))) %>% + # count_df(., translate_ab = "name", language = language) + # }} } cat('Implicit join in get_resistance_df(..) @server.R:692\n') @@ -735,8 +750,9 @@ server <- function(input, output, session) { percent_si = percent(SI/all, 0.1)) %>% pivot_longer(cols = c("SI", "R"), names_to = "interpretation", values_to = "value") %>% mutate(mo = as.mo(input$patho_plot_selected)) %>% - left_join(intrinsic_info) %>% - mutate(flag = if_else(intrinsic_r == TRUE, "(intrinsic resistance)", NA_character_)) + mutate(flag = "") + # left_join(intrinsic_info) %>% + # mutate(flag = if_else(intrinsic_r == TRUE, "(intrinsic resistance)", NA_character_)) }) @@ -761,6 +777,7 @@ server <- function(input, output, session) { values = c("#FDE725FF", "#440154FF"), na.value = "lightgrey") + scale_x_continuous(labels = percent) + + # flag not used at the moment - for intrinsic resistance geom_text(data = isolate_prop_data(), aes(0.5, reorder(antibiotic, value_r), label = flag), colour = "red") + ggtitle(label = paste0("Selected isolates: *", mo_fullname(as.mo(input$patho_plot_selected)), "*"), subtitle = if (any(isolate_prop_data()$all < 30)) {