changes for paper revisions

analysis/12_plot_samples.R

@@ -18,7 +18,7 @@ library(here)
 library(STAVE)
 
 # read in combined STAVE object
-s <- readRDS(here("analysis", "data-out", "stave_data_2026.03.13.rds"))
+s <- readRDS(here("analysis", "data-out", "stave_data_2026.03.17.rds"))
 
 # get WHO positions
 k13_dictionary <- read.csv(here("analysis", "data-raw", "k13_ref_protein_codon_dictionary.csv")) |>

analysis/14_make_summary.R

@@ -0,0 +1,70 @@
+# 14_make_summary.R
+#
+# Author: Bob Verity
+# Date: 2026-03-19
+#
+# Purpose:
+# Makes a .xlsx version of the STAVE prevalence data for the supplementary materials.
+#
+# ------------------------------------------------------------------
+
+fix_encoding <- function(df) {
+  is_chr <- vapply(df, is.character, logical(1))
+  df[is_chr] <- lapply(df[is_chr], function(x) {
+    iconv(x, from = "", to = "UTF-8")
+  })
+  names(df) <- iconv(names(df), from = "", to = "UTF-8")
+  df
+}
+
+insert_name <- function(x, name, pos) {
+  x <- x[x != name]              # remove if already present
+  append(x, name, after = pos - 1)
+}
+
+# ------------------------------------------------------------------
+
+library(openxlsx)
+library(readxl)
+library(writexl)
+library(stringi)
+
+# read in combined STAVE object and existing summary xlsx
+s <- readRDS(here("analysis", "data-out", "stave_data_2026.03.17.rds"))
+summary_xl_path <- here("analysis", "data-out", "marker_prevalence_2026.03.17.xlsx")
+
+s
+
+# open connection to summary xlsx
+wb <- openxlsx::loadWorkbook(summary_xl_path)
+
+# replace studies sheet
+removeWorksheet(wb, "studies")
+addWorksheet(wb, "studies")
+writeData(wb, "studies", fix_encoding(s$get_studies()))
+
+# replace surveys sheet
+removeWorksheet(wb, "surveys")
+addWorksheet(wb, "surveys")
+writeData(wb, "surveys", fix_encoding(s$get_surveys()))
+
+# get data for all mutations
+mut_names <- c("crt_76_T", "mdr1_86_Y", "k13_446_I", "k13_469_Y", "k13_476_I",
+               "k13_493_H", "k13_539_T", "k13_553_L", "k13_561_H", "k13_574_L",
+               "k13_580_Y", "k13_622_I", "k13_675_V", "k13_441_L", "k13_449_A",
+               "k13_469_F", "k13_515_K", "k13_527_H", "k13_538_V", "k13_568_G")
+
+for (i in seq_along(mut_names)) {
+  message(sprintf("%s of %s", i, length(mut_names)))
+
+  df_mut <- s$get_prevalence(target_variant = gsub("_", ":", mut_names[i])) |>
+    select(study_id, survey_id, numerator, denominator, prevalence, prevalence_lower, prevalence_upper)
+
+  removeWorksheet(wb, mut_names[i])
+  addWorksheet(wb, mut_names[i])
+  writeData(wb, mut_names[i], df_mut)
+}
+
+# save (overwrite file)
+saveWorkbook(wb, summary_xl_path, overwrite = TRUE)
+