In eric-hunt/uncleR: an R package for parsing UNcle data

# set chunk defaults for suppressing console message and displaying code by default
knitr::opts_chunk$set(
  message = FALSE,
  # warning = FALSE,
  echo = TRUE,
  include = TRUE
)
# set working directory for chunks and show progress bar for knitr actions
knitr::opts_knit$set(
  root.dir = "~/OneDrive - New England Biolabs/Documents/AppDev/Uncle Data Analysis/DataPrep/",
  progress = TRUE
)


## data loading and manipulation
# library(feather)
library(tidyverse)
# library(magrittr) # for the Tee pipe
library(readxl)

## statistics
# library(rstatix)

## plotting
library(cowplot)
# library(ggrepel)
# library(ggridges)
# library(gganimate)
# library(lemon)
library(RColorBrewer)
library(xkcdcolors)
library(extrafont)

## programming
library(glue)
library(rlang)

## interactivity
# library(crosstalk)
# library(plotly)

# user packages
# library(fragr)
library(UNcleR)
# library(RTtools)

# default style for ggplot
theme_set(
  theme_bw(base_family = "Roboto Condensed") +
    theme(
      axis.text = element_text(face = "bold"),
      panel.grid = element_blank()
    )
)


# useful variables
wellOrder <- purrr::map2_chr(rep(c(LETTERS[1:8]), 12), purrr::flatten_chr(purrr::map(c(1:12), rep, 8)), paste0)
uniOrder <- purrr::map2_chr(rep(c(LETTERS[1:16]), 3), purrr::flatten_chr(purrr::map(c(1:3), rep, 16)), paste0)

Consolidating Experimental Data

A function should be developed to serve as a single tool for consolidating all experimental data based on directory hierarchy. Currently, single-use or anonymous functions are written to import Uncle data and package it for the dashboard.

run_info <- list(
  user = "Eric Hunt",
  date = lubridate::today(),
  protein_full = "Bst 2.0 Polymerase",
  protein_abbrev = "Bst2Pol"
)

experiments <- list(
  "General" = glue::glue("{run_info$protein_abbrev}/Exports/General Screen/"),
  "pH" = glue::glue("{run_info$protein_abbrev}/Exports/pH Screen/")
)

consolidate_experiments <- function(prot_dir, join_vars = NULL, legacy = FALSE, SLSheader = TRUE, DLSheader = FALSE) {
  if (!(dir.exists(prot_dir))) {
    stop("The provided protein directory does not exist.")
  }
  if (!(dir.exists(paste0(prot_dir, "/", "Exports")))) {
    stop("There is no 'Exports' subdirectory. Where are the export files?")
  }

  if (is.null(join_vars)) {
    join_vars <- c("date", "instrument", "protein", "plate", "uni")
  }

  dirList <- list.dirs(paste0(prot_dir, "/Exports/"), full.names = TRUE, recursive = FALSE) |>
  rlang::set_names(nm = list.dirs(paste0(prot_dir, "/Exports/"), full.names = FALSE, recursive = FALSE))

  import_experiment <- function(dir, protein) {
    if (legacy) {
      importList <- list(
        FLUORspec = UNcleR::import_FLUORspec(dir),
        SLSsum = UNcleR::import_SLSsum(dir, header = SLSheader),
        SLSspec266 = UNcleR::import_SLSspec(dir, lambda = 266),
        SLSspec473 = UNcleR::import_SLSspec(dir, lambda = 473),
        DLSsum = UNcleR::import_DLSsum(dir, header = DLSheader),
        DLSspecC = UNcleR::import_DLSspec(dir, pattern = "DLS Spec C", type = "C"),
        DLSspecI = UNcleR::import_DLSspec(dir, pattern = "DLS Spec I", type = "I"),
        DLSspecM = UNcleR::import_DLSspec(dir, pattern = "DLS Spec M", type = "M")
      )
    } else {
      importList <- list(
        SLSsum = UNcleR::import_SLSsum(dir, header = SLSheader),
        DLSsum = UNcleR::import_DLSsum(dir, header = DLSheader),
        specStatic = UNcleR::import_staticBundle(dir),
        specDynamic = UNcleR::import_dynamicBundle(dir)
      )
    }
    purrr::reduce(
      importList,
      dplyr::full_join,
      by = join_vars
    ) |>
    dplyr::select(-tidyselect::contains("sample"), -tidyselect::contains("file")) |> {
      \(df) dplyr::mutate(
        df,
        plate = stringr::str_trim(df$plate, side = "both"),
        protein = protein
      )
    }()
  }

  consolidated <- purrr::map(
    dirList,
    \(dir) import_experiment(dir, prot_dir)
  ) # |> rlang::set_names(nm = names(expList))

  return(consolidated)
}

test <- consolidate_experiments("Bst2Pol")

eric-hunt/uncleR documentation built on Dec. 20, 2021, 5:28 a.m.