Prepare for using AMR version 1.8.2: remove left_join(intrinsic_info), recognize co-trimoxazol
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5
global.R
5
global.R
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@ -39,7 +39,8 @@ tAntibiotics = readxl::read_xlsx('data/ab_mapping.xlsx') %>%
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# radar_data <- readGlimsArchive(ymdStartDate = ymdStartDate,
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# radar_data <- readGlimsArchive(ymdStartDate = ymdStartDate,
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# ymdEndDate = ymdEndDate,
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# ymdEndDate = ymdEndDate,
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# readPreprocessed = T)
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# readPreprocessed = T)
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radar_data <- readGlimsFinalResults()
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radar_data <- readGlimsFinalResults() %>%
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mutate_if(is.rsi, as.sir)
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if (!'CRO' %in% colnames(radar_data))
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if (!'CRO' %in% colnames(radar_data))
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radar_data <- radar_data %>% add_column('CRO' = '')
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radar_data <- radar_data %>% add_column('CRO' = '')
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@ -85,7 +86,7 @@ suppressMessages(
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)
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)
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intrinsic_info <- AMR::intrinsic_resistant %>%
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intrinsic_info <- AMR::intrinsic_resistant %>%
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mutate(mo = as.mo(microorganism),
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mutate(#mo = as.mo(microorganism),
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intrinsic_r = TRUE)
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intrinsic_r = TRUE)
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35
server.R
35
server.R
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@ -696,13 +696,28 @@ server <- function(input, output, session) {
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"Vancomycin")
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"Vancomycin")
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get_resistance_df <- function(.data, mo_selected, abx, language = "en") {
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get_resistance_df <- function(.data, mo_selected, abx, language = "en") {
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.data %>%
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filter(mo == as.mo(mo_selected)) %>%
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out <- .data %>%
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{if (nrow(.) != 0) {
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filter(mo == as.mo(mo_selected))
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group_by_at(., input$box1.2_group) %>%
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select(group_vars(.), as.character(as.ab(abx))) %>%
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print(paste("rijen voor ", mo_selected, ":", nrow(out)))
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count_df(., translate_ab = "name", language = language)
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abx <- gsub("Co-trimoxazole", "Trimetoprim / sufamethoxazole", abx)
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}}
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if (nrow(out) > 0) {
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out %>%
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select(mo, as.character(as.ab(abx))) %>%
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count_df(., translate_ab = "name", language = language)
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} else {
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out
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}
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# .data %>%
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# filter(mo == as.mo(mo_selected)) %>%
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# {if (nrow(.) != 0) {
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# group_by_at(., input$box1.2_group) %>%
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# select(group_vars(.), as.character(as.ab(abx))) %>%
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# count_df(., translate_ab = "name", language = language)
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# }}
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}
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}
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cat('Implicit join in get_resistance_df(..) @server.R:692\n')
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cat('Implicit join in get_resistance_df(..) @server.R:692\n')
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@ -735,8 +750,9 @@ server <- function(input, output, session) {
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percent_si = percent(SI/all, 0.1)) %>%
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percent_si = percent(SI/all, 0.1)) %>%
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pivot_longer(cols = c("SI", "R"), names_to = "interpretation", values_to = "value") %>%
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pivot_longer(cols = c("SI", "R"), names_to = "interpretation", values_to = "value") %>%
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mutate(mo = as.mo(input$patho_plot_selected)) %>%
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mutate(mo = as.mo(input$patho_plot_selected)) %>%
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left_join(intrinsic_info) %>%
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mutate(flag = "")
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mutate(flag = if_else(intrinsic_r == TRUE, "(intrinsic resistance)", NA_character_))
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# left_join(intrinsic_info) %>%
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# mutate(flag = if_else(intrinsic_r == TRUE, "(intrinsic resistance)", NA_character_))
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})
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})
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@ -761,6 +777,7 @@ server <- function(input, output, session) {
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values = c("#FDE725FF", "#440154FF"),
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values = c("#FDE725FF", "#440154FF"),
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na.value = "lightgrey") +
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na.value = "lightgrey") +
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scale_x_continuous(labels = percent) +
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scale_x_continuous(labels = percent) +
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# flag not used at the moment - for intrinsic resistance
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geom_text(data = isolate_prop_data(), aes(0.5, reorder(antibiotic, value_r), label = flag), colour = "red") +
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geom_text(data = isolate_prop_data(), aes(0.5, reorder(antibiotic, value_r), label = flag), colour = "red") +
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ggtitle(label = paste0("Selected isolates: *", mo_fullname(as.mo(input$patho_plot_selected)), "*"),
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ggtitle(label = paste0("Selected isolates: *", mo_fullname(as.mo(input$patho_plot_selected)), "*"),
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subtitle = if (any(isolate_prop_data()$all < 30)) {
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subtitle = if (any(isolate_prop_data()$all < 30)) {
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