ENH: Create control well filelist to optimize CellProfiler pipeline

src/filelist-controls.R

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+suppressPackageStartupMessages({
+    library(tidyverse)
+    library(magrittr)
+    library(readxl)
+    library(stringr)
+    library(methods) # For Rscript per http://stackoverflow.com/a/41797025
+})
+
+## Configuration values.
+files_plate <- "../data/DRSC_TF_Library_Distribution.xls"
+path_images <- "../results/z_projection"
+file_filelist <- "../results/cellprofiler/2017-02-20/filelist"
+
+## Plate 504 was run at the last minute, and so the controls are not
+## reflected in the Excel spreadsheet provided by the core facility.
+## Therefore below is the list of added wells, which we will later
+## merge with the spreadsheet data:
+wells_control <- tibble::tribble(
+    ~well, ~symbol,
+    ##---|------
+    "I04", "BROWN",
+    "E09", "CAL1",
+    "L03", "FACT",
+    "E16", "Rho1",
+    "L16", "Thread",
+    "H21", "water") %>%
+    bind_rows(tibble(
+        symbol = "LacZ",
+        well = c("C03", "C22", "D12", "D13", "E05", "E20", "F11",
+                 "F14", "G07", "G18", "H09", "H16", "I09", "I16",
+                 "J07", "J18", "K11", "K14", "L05", "L20", "M12",
+                 "M13", "N03", "N22"))) %>%
+    rename(symbol_control = symbol) %>% # Prepare for join.
+    arrange(well)
+## FIXME: Need to confirm what type of control Thread is.
+wells_layout <-
+    read_excel(files_plate, sheet = 3) %>%
+    setNames(tolower(names(.))) %>%
+    select(plate, well, `symbol(s)`, `fbgn(s)`, amplicon) %>%
+    rename(symbol = `symbol(s)`,
+           fbgn = `fbgn(s)`) %>% arrange(plate, well)
+wells_layout %<>%
+    left_join(wells_control) %>%
+    mutate(symbol = ifelse(is.na(symbol_control), symbol, symbol_control)) %>%
+    select(-symbol_control) %>%
+    mutate(control = ifelse(
+               symbol %in% c("CAL1", "FACT", "Rho1"), ## Rho1 gives binucleates
+               "positive", NA)) %>%
+    mutate(control = ifelse(
+               symbol %in% c("LacZ", "Empty", "BROWN", "water"),
+               "negative", control)) %>%
+    mutate(control = ifelse(
+               is.na(control) & is.na(amplicon),
+               "unknown", control))
+
+## List all controls
+wells_control <- wells_layout %>%
+    filter(!is.na(control)) %>%
+    mutate(plate = ifelse(plate == "504", "160415_015529-V", plate)) %>%
+    mutate(file_glob = paste0(plate, "*_", well, "_*"))
+
+## Glob for files
+filelist <- Sys.glob(file.path(normalizePath(path_images),
+                               wells_control$file_glob))
+
+## Save the list
+writeLines(filelist, file_filelist)