filelist-controls.R

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)