In matthieu-haudiquet/rothSGA: Rothstein Lab SGA Analysis Tools

knitr::opts_chunk$set(message = FALSE)

Setup

library(tidyverse)
library(rothSGA)
dir = params$dir
bio_rep_file            = file.path(dir, params$bio_rep_file)
processed_colonies_file = file.path(dir, params$processed_colonies_file)
processed_strains_file  = file.path(dir, params$processed_strains_file)

Annotate Images

screenmill::annotate(dir, overwrite = params$re_annotate)
add_biological_replicates(dir, file = params$bio_rep_file)

Calibrate, measure, and review colonies

screenmill::calibrate(dir, overwrite = params$re_calibrate)
screenmill::measure(dir, overwrite = params$re_measure)
screenmill::review(dir, overwrite = params$needs_review)

Apply normalizations

data_all <-
  screenmill::read_screenmill(dir) %>%
  left_join(read_csv(bio_rep_file, col_types = cols()), by = c("plate_id", "query_name", "query_id", "group", "position")) %>%
  exclude_large_colonies(thresh = 1.5) %>%
  normalize_spatial_effect(of = 'size', death_thresh = 0.25, prefix = 'size_') %>%
  normalize_plate_effect(of = 'size_spatial_norm', prefix = 'size_spatial_') %>%
  write_csv(processed_colonies_file)

data_bio_reps <-
  data_all %>%
  # Custom cisplatin annotation
  mutate(cisplatin = as.numeric(stringr::str_extract(treatment_id, "(?<=-).*(?=(uM))"))) %>%
  # Custom aggregation
  group_by(
    # Level of aggregation should identify each strain
    plate_id, bio_replicate, plate, row, column,
    # Other annotation features
    date, hours_growth,
    strain_collection_id, strain_id, gene_id, query_id, treatment_id,
    strain_name, query_name, cisplatin
  ) %>%
  summarise(
    n_tech             = n(), # exclusions have already been removed
    plate_control_mean = mean(size_spatial_plate_effect),
    mean_size_norm     = mean(size_spatial_plate_norm),
    median_size_norm   = median(size_spatial_plate_norm),
    sd_size_norm       = sd(size_spatial_plate_norm)
  ) %>%
  ungroup() %>%
  write_csv(processed_strains_file)

Session

options(width = 90)
devtools::session_info()

matthieu-haudiquet/rothSGA documentation built on May 14, 2019, 11:28 a.m.