## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----echo=FALSE, results="hide", message=FALSE-------------------------------- ("badger") ## ----normfluodat, eval=F------------------------------------------------------ # # Normal cases dat(1-4) # fpath <- system.file("extdata", "dat_2.dat", package = "normfluodbf", mustWork = TRUE) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40, rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40, rows_used = c('A','B','C'), interval = 30) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40, rows_used = c('A','B','C'), interval = 60) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3)) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'horizontal') # # # Extreme cases dat(5-7) # fpath <- system.file("extdata", "dat_5.dat", package = "normfluodbf", mustWork = TRUE) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A'), cols_used = c(1)) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A'), cols_used = c(1,2)) # # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3)) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'horizontal') ## ----normfluodatlite, eval=F-------------------------------------------------- # # Normal cases dat(1-4) # fpath <- system.file("extdata", "dat_1.dat", package = "normfluodbf", mustWork = TRUE) # normalized_fluo_dat <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'hundred') # normalized_fluo_dat <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'one') # normalized_fluo_dat <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40) # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3)) # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'horizontal') # # # Extreme cases dat(5-7) # fpath <- system.file("extdata", "dat_5.dat", package = "normfluodbf", mustWork = TRUE) # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40) # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3)) # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3)) # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3)) # # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3)) # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluodatlite(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'horizontal') ## ----normfluodatfull, eval=F-------------------------------------------------- # # Normal cases dat(1-4) # fpath <- system.file("extdata", "dat_3.dat", package = "normfluodbf", mustWork = TRUE) # normalized_fluo_dat <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'hundred') # normalized_fluo_dat <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'one') # normalized_fluo_dat <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40) # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3)) # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'horizontal') # # # Extreme cases dat(5-7) # fpath <- system.file("extdata", "dat_6.dat", package = "normfluodbf", mustWork = TRUE) # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal', norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'hundred') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'one') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'z-score') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'decimal') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), norm_scale = 'raw') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40) # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3)) # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluodatfull(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'horizontal') # ## ----normfluordat, eval=F----------------------------------------------------- # # Normal cases dat(1-4) # fpath <- system.file("extdata", "dat_3.dat", package = "normfluodbf", mustWork = TRUE) # normalized_fluo_dat <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3)) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'horizontal') # # # Extreme cases dat(5-7) # fpath <- system.file("extdata", "dat_5.dat", package = "normfluodbf", mustWork = TRUE) # normalized_fluo_dat <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), read_direction = 'horizontal') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C')) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3)) # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'vertical') # normalized_fluo_dat_advv <- normfluordat(dat=fpath, tnp = 1, cycles = 40,rows_used = c('A','B','C'), cols_used = c(1,2,3), read_direction = 'horizontal') ## ----normfluordbf, eval=F----------------------------------------------------- # #normfluordbf # fpath <- system.file("extdata", "liposomes_214.dbf", package = "normfluodbf", mustWork = TRUE) # norm_dbf <- normfluordbf(fpath, norm_scale = 'raw') # norm_dbf <- normfluordbf(fpath, norm_scale = 'decimal') # norm_dbf <- normfluordbf(fpath, norm_scale = 'one') # norm_dbf <- normfluordbf(fpath, norm_scale = 'hundred') # norm_dbf <- normfluordbf(fpath, norm_scale = 'z-score') ## ----norm_tidy_dbf, eval=F---------------------------------------------------- # #norm_tidy_dbf # fpath <- system.file("extdata", "liposomes_214.dbf", package = "normfluodbf", mustWork = TRUE) # norm_dbf <- norm_tidy_dbf(fpath, norm_scale = 'raw') # norm_dbf <- norm_tidy_dbf(fpath, norm_scale = 'decimal') # norm_dbf <- norm_tidy_dbf(fpath, norm_scale = 'one') # norm_dbf <- norm_tidy_dbf(fpath, norm_scale = 'hundred') # norm_dbf <- norm_tidy_dbf(fpath, norm_scale = 'z-score') ## ----time_attribute, eval=F--------------------------------------------------- # #Time attribute # #214 # time_original = time_attribute(30,8,136,1276,40) # norm_dbf = cbind(time_original,norm_dbf) # #221 # time_original = time_attribute(33,8,907,2161,40) # norm_dbf = cbind(time_original,norm_dbf) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'one', interval = 30, first_end = 8, pause_duration = 136, end_time = 1276) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'one', interval = 33, first_end = 8, pause_duration = 0, end_time = 2161) # normalized_fluo_dat_advv <- normfluodat(dat=fpath, tnp = 3, cycles = 40,rows_used = c('A','B','C'), read_direction = 'vertical', norm_scale = 'one', interval = 33) # for (i in 1:nrow(normalized_fluo_dat_advv)) { # for(j in 1:ncol(normalized_fluo_dat_advv)) # if(j == 1){ # normalized_fluo_dat_advv[i,j] = normalized_fluo_dat_advv[i,j] + 30 # } # } ## ----ggplot_tnp, eval=F------------------------------------------------------- # #Visualize # # #DAT # #z-score # ggplot_tnp(normalized_fluo_dat, c('Cycle_Number'), c('A1','B1','C1'),c(0,40),c(-1,3)) # # #hundred # ggplot_tnp(normalized_fluo_dat, c('Cycle_Number'), c('A1','B1','C1'),c(0,40),c(0,100)) # # #one # ggplot_tnp(normalized_fluo_dat, c('Cycle_Number'), c('A1','B1','C1'),c(0,40),c(0,1)) # # #raw & decimal (sliding scale) # ggplot_tnp(normalized_fluo_dat, c('Cycle_Number'), c('A1','B1','C1'),c(0,40),ylim = NULL) # # #DBF # ggplot_tnp(norm_dbf, c('Cycle_Number'), c('A01','B01','C01'),c(0,40),ylim = NULL) # ggplot_tnp(norm_dbf, c('Time'), c('A01','B01','C01'),xlim = NULL, ylim = NULL)