Nothing
## normfluodbf - R package that Cleans and Normalizes FLUOstar DBF and DAT Files
## Copyright (C) 2024 Tingwei Adeck
#' Plate Data
#' @family platedata
#' @param file file
#' @param tnp tnp
#' @param cycles cycles
#' @param rows_used rows_used
#' @param ... dots
#' @return plate data
#' @name platedata
#' @examples
#' \dontrun{plate_data(file, tnp, cycles, rows_used = c(A,B,C), norm_scale = 'raw')}
NULL
#' @rdname platedata
#' @return plate data
#' @export
plate_data = function(file, tnp = NULL, cycles = NULL, rows_used = NULL,...){
if(grepl("\\.dbf$", file)){
df = suppressMessages({normfluordbf(file, ...)})
new_names = remove_leading_zero(names(df))
colnames(df) <- new_names
class(df) = c("normfluodbf_dbf", class(df))
df
} else {
if (is.null(tnp) || is.null(cycles))
rlang::abort(sprintf('DAT:The params %s and %s must be provided and for making plates it is advised to provide %s', 'tnp', 'cycles', 'rows_used'));
df = suppressMessages({normfluodat(file, tnp, cycles, rows_used, ...) })
class(df) = c("normfluodbf_dat", class(df))
df
}
}
#' Format Plate Data
#' @family formatplatedata
#' @param plate plate
#' @return plate
#' @name formatplatedata
#' @examples
#' \dontrun{format_plate_data(plate)}
NULL
#' @rdname formatplatedata
#' @return plate
#' @export
format_plate_data <- function(plate){
UseMethod("format_plate_data")
}
#' @rdname formatplatedata
#' @return plate
#' @export
format_plate_data.default = function(plate){
CURRENT_STEP <- plate %>% step('FORMAT_DATA')
#plate %>% check_step(CURRENT_STEP)
step_begin('Formating Plate Data')
phd = plate[['plate_data']]
phd %>% tibble::as_tibble()
if (assertthat::are_equal(colnames(phd[,c(1,2)]), c("Time","Cycle_Number")) ){
pfd = cbind( phd[1:2],
stack(phd[3:ncol(phd)]) )
names(pfd)[3:ncol(pfd)] <- c('fluor_values','well')
if(is_normalized(pfd)){
pfd = pfd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)),
"sample" = well,
"used" = TRUE,
"outlier" = FALSE) %>%
dplyr::select("well", "sample", "well_row", "well_col", "used", "Cycle_Number", "Time", "fluor_values", "outlier")
message('Cannot check for outliers in already normalized plate data')
}
else {
pfd = detect_outliers_time_cn(plate = plate, data = pfd)
}
load_plate_data(plate) = pfd
status(plate) = define_status(plate)[['FORMAT_DATA']]
steps(plate) = plate[['steps']][-1]
step_end('Data Formatted')
plate
#return(pfd)
} else {
pfd = cbind( phd[1],
stack(phd[2:ncol(phd)]) )
names(pfd)[2:ncol(pfd)] <- c('fluor_values','well')
if(is_normalized(pfd)){
pfd = pfd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)),
"sample" = well,
"used" = TRUE,
"outlier" = FALSE) %>%
dplyr::select("well", "sample", "well_row", "well_col", "used", "Cycle_Number", "Time", "fluor_values", "outlier")
message('Cannot check for outliers in already normalized plate data')
}
else {
pfd = detect_outliers_cn(plate = plate, data = pfd)
}
load_plate_data(plate) = pfd
status(plate) = define_status(plate)[['FORMAT_DATA']]
steps(plate) = plate[['steps']][-1]
step_end('Data Formatted')
plate
#return(pfd)
}
}
#' @rdname formatplatedata
#' @return plate
#' @export
format_plate_data.96well_plate = function(plate){
CURRENT_STEP <- plate %>% step('FORMAT_DATA')
#plate %>% check_step(CURRENT_STEP)
step_begin('Formating Plate Data')
phd = plate[['plate_data']]
phd %>% tibble::as_tibble()
if (assertthat::are_equal(colnames(phd[,c(1,2)]), c("Time","Cycle_Number")) ){
pfd = cbind( phd[1:2],
stack(phd[3:ncol(phd)]) )
names(pfd)[3:ncol(pfd)] <- c('fluor_values','well')
if(is_normalized(pfd)){
pfd = pfd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)),
"sample" = well,
"used" = TRUE,
"outlier" = FALSE) %>%
dplyr::select("well", "sample", "well_row", "well_col", "used", "Cycle_Number", "Time", "fluor_values", "outlier")
message('Cannot check for outliers in already normalized plate data')
}
else {
pfd = detect_outliers_time_cn(plate = plate, data = pfd)
}
load_plate_data(plate) = pfd
status(plate) = define_status(plate)[['FORMAT_DATA']]
steps(plate) = plate[['steps']][-1]
step_end('Data Formatted')
plate
#return(pfd)
} else {
pfd = cbind( phd[1],
stack(phd[2:ncol(phd)]) )
names(pfd)[2:ncol(pfd)] <- c('fluor_values','well')
if(is_normalized(pfd)){
pfd = pfd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)),
"sample" = well,
"used" = TRUE,
"outlier" = FALSE) %>%
dplyr::select("well", "sample", "well_row", "well_col", "used", "Cycle_Number", "Time", "fluor_values", "outlier")
message('Cannot check for outliers in already normalized plate data')
}
else {
pfd = detect_outliers_cn(plate = plate, data = pfd)
}
load_plate_data(plate) = pfd
status(plate) = define_status(plate)[['FORMAT_DATA']]
steps(plate) = plate[['steps']][-1]
step_end('Data Formatted')
plate
#return(pfd)
}
}
#' @rdname formatplatedata
#' @return plate
#' @export
format_plate_data.384well_plate = function(plate){
CURRENT_STEP <- plate %>% step('FORMAT_DATA')
#plate %>% check_step(CURRENT_STEP)
step_begin('Formating Plate Data')
phd = plate[['plate_data']]
phd %>% tibble::as_tibble()
if (assertthat::are_equal(colnames(phd[,c(1,2)]), c("Time","Cycle_Number")) ){
pfd = cbind( phd[1:2],
stack(phd[3:ncol(phd)]) )
names(pfd)[3:ncol(pfd)] <- c('fluor_values','well')
if(is_normalized(pfd)){
pfd = pfd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)),
"sample" = well,
"used" = TRUE,
"outlier" = FALSE) %>%
dplyr::select("well", "sample", "well_row", "well_col", "used", "Cycle_Number", "Time", "fluor_values", "outlier")
message('Cannot check for outliers in already normalized plate data')
}
else {
pfd = detect_outliers_time_cn(plate = plate, data = pfd)
}
load_plate_data(plate) = pfd
status(plate) = define_status(plate)[['FORMAT_DATA']]
steps(plate) = plate[['steps']][-1]
step_end('Data Formatted')
plate
#return(pfd)
} else {
pfd = cbind( phd[1],
stack(phd[2:ncol(phd)]) )
names(pfd)[2:ncol(pfd)] <- c('fluor_values','well')
if(is_normalized(pfd)){
pfd = pfd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)),
"sample" = well,
"used" = TRUE,
"outlier" = FALSE) %>%
dplyr::select("well", "sample", "well_row", "well_col", "used", "Cycle_Number", "Time", "fluor_values", "outlier")
message('Cannot check for outliers in already normalized plate data')
}
else {
pfd = detect_outliers_cn(plate = plate, data = pfd)
}
load_plate_data(plate) = pfd
status(plate) = define_status(plate)[['FORMAT_DATA']]
steps(plate) = plate[['steps']][-1]
step_end('Data Formatted')
plate
#return(pfd)
}
}
#' @rdname formatplatedata
#' @return plate
#' @export
format_plate_data.1536well_plate_t1 = function(plate){
CURRENT_STEP <- plate %>% step('FORMAT_DATA')
#plate %>% check_step(CURRENT_STEP)
step_begin('Formating Plate Data')
phd = plate[['plate_data']]
phd %>% tibble::as_tibble()
if (assertthat::are_equal(colnames(phd[,c(1,2)]), c("Time","Cycle_Number")) ){
pfd = cbind( phd[1:2],
stack(phd[3:ncol(phd)]) )
names(pfd)[3:ncol(pfd)] <- c('fluor_values','well')
if(is_normalized(pfd)){
pfd = pfd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)),
"sample" = well,
"used" = TRUE,
"outlier" = FALSE) %>%
dplyr::select("well", "sample", "well_row", "well_col", "used", "Cycle_Number", "Time", "fluor_values", "outlier")
message('Cannot check for outliers in already normalized plate data')
}
else {
pfd = detect_outliers_time_cn(plate = plate, data = pfd)
}
load_plate_data(plate) = pfd
status(plate) = define_status(plate)[['FORMAT_DATA']]
steps(plate) = plate[['steps']][-1]
step_end('Data Formatted')
plate
#return(pfd)
} else {
pfd = cbind( phd[1],
stack(phd[2:ncol(phd)]) )
names(pfd)[2:ncol(pfd)] <- c('fluor_values','well')
if(is_normalized(pfd)){
pfd = pfd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)),
"sample" = well,
"used" = TRUE,
"outlier" = FALSE) %>%
dplyr::select("well", "sample", "well_row", "well_col", "used", "Cycle_Number", "Time", "fluor_values", "outlier")
message('Cannot check for outliers in already normalized plate data')
}
else {
pfd = detect_outliers_cn(plate = plate, data = pfd)
}
load_plate_data(plate) = pfd
status(plate) = define_status(plate)[['FORMAT_DATA']]
steps(plate) = plate[['steps']][-1]
step_end('Data Formatted')
plate
#return(pfd)
}
}
#' @rdname formatplatedata
#' @return plate
#' @export
format_plate_data.1536well_plate_t2 = function(plate){
CURRENT_STEP <- plate %>% step('FORMAT_DATA')
#plate %>% check_step(CURRENT_STEP)
step_begin('Formating Plate Data')
phd = plate[['plate_data']]
phd %>% tibble::as_tibble()
if (assertthat::are_equal(colnames(phd[,c(1,2)]), c("Time","Cycle_Number")) ){
pfd = cbind( phd[1:2],
stack(phd[3:ncol(phd)]) )
names(pfd)[3:ncol(pfd)] <- c('fluor_values','well')
if(is_normalized(pfd)){
pfd = pfd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)),
"sample" = well,
"used" = TRUE,
"outlier" = FALSE) %>%
dplyr::select("well", "sample", "well_row", "well_col", "used", "Cycle_Number", "Time", "fluor_values", "outlier")
message('Cannot check for outliers in already normalized plate data')
}
else {
pfd = detect_outliers_time_cn(plate = plate, data = pfd)
}
load_plate_data(plate) = pfd
status(plate) = define_status(plate)[['FORMAT_DATA']]
steps(plate) = plate[['steps']][-1]
step_end('Data Formatted')
plate
#return(pfd)
} else {
pfd = cbind( phd[1],
stack(phd[2:ncol(phd)]) )
names(pfd)[2:ncol(pfd)] <- c('fluor_values','well')
if(is_normalized(pfd)){
pfd = pfd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)),
"sample" = well,
"used" = TRUE,
"outlier" = FALSE) %>%
dplyr::select("well", "sample", "well_row", "well_col", "used", "Cycle_Number", "Time", "fluor_values", "outlier")
message('Cannot check for outliers in already normalized plate data')
}
else {
pfd = detect_outliers_cn(plate = plate, data = pfd)
}
load_plate_data(plate) = pfd
status(plate) = define_status(plate)[['FORMAT_DATA']]
steps(plate) = plate[['steps']][-1]
step_end('Data Formatted')
plate
#return(pfd)
}
}
#' Modify Plate Data
#' @family modifyplatedata
#' @param plate plate
#' @return plate
#' @name modifyplatedata
#' @examples
#' \dontrun{modify_plate_meta(plate)}
NULL
#' @rdname modifyplatedata
#' @return plate
#' @export
modify_plate_data <- function(plate){
UseMethod("modify_plate_data")
}
#' @rdname modifyplatedata
#' @return plate
#' @export
modify_plate_data.default = function(plate){
CURRENT_STEP <- plate %>% step('MODIFY_DATA')
cols_to_remove = 'sample'; bycol = "well"
jd <- dplyr::left_join(plate[['plate_meta']],
plate[['plate_data']],
suffix = c("",""), #can also use original vs new suffix
by = bycol) #multiple = "all" for full joins
if(!is.null(cols_to_remove)){
jd <- jd %>% dplyr::select(!all_of(c(cols_to_remove)))
jd %<>% dplyr::mutate(used = if_else(is.na(used), FALSE, TRUE), .keep = "all")
jd %<>% dplyr::arrange(desc(used), well_row, well_col)
jd = jd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)))
class(jd) = c("mod_normfluodbf_data", class(jd))
jd
load_plate_data(plate) = jd
status(plate) = define_status(plate)[['MODIFY_DATA']]
steps(plate) = plate[['steps']][-1]
plate
}
else {
jd %<>% mutate(used = if_else(is.na(used), FALSE, TRUE), .keep = "all")
jd = jd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)))
class(jd) = c("mod_normfluodbf_data", class(jd))
jd
load_plate_data(plate) = jd
status(plate) = define_status(plate)[['MODIFY_DATA']]
steps(plate) = plate[['steps']][-1]
plate
}
}
#' @rdname modifyplatedata
#' @return plate
#' @export
modify_plate_data.96well_plate = function(plate){
CURRENT_STEP <- plate %>% step('MODIFY_DATA')
cols_to_remove = 'sample'; bycol = "well"
jd <- dplyr::left_join(plate[['plate_meta']],
plate[['plate_data']],
suffix = c("",""), #can also use original vs new suffix
by = bycol
) #multiple = "all" for full joins
if(!is.null(cols_to_remove)){
jd <- jd %>% dplyr::select(!all_of(c(cols_to_remove)))
jd %<>% dplyr::mutate(used = if_else(is.na(used), FALSE, TRUE), .keep = "all")
jd %<>% dplyr::arrange(desc(used), well_row, well_col)
jd = jd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)))
class(jd) = c("mod_normfluodbf_data", class(jd))
jd
load_plate_data(plate) = jd
status(plate) = define_status(plate)[['MODIFY_DATA']]
steps(plate) = plate[['steps']][-1]
plate
}
else {
jd %<>% mutate(used = if_else(is.na(used), FALSE, TRUE), .keep = "all")
jd = jd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)))
class(jd) = c("mod_normfluodbf_data", class(jd))
jd
load_plate_data(plate) = jd
status(plate) = define_status(plate)[['MODIFY_DATA']]
steps(plate) = plate[['steps']][-1]
plate
}
}
#' @rdname modifyplatedata
#' @return plate
#' @export
modify_plate_data.384well_plate = function(plate){
CURRENT_STEP <- plate %>% step('MODIFY_DATA')
cols_to_remove = 'sample'; bycol = "well"
jd <- dplyr::left_join(plate[['plate_meta']],
plate[['plate_data']],
suffix = c("",""), #can also use original vs new suffix
by = bycol
) #multiple = "all" for full joins
if(!is.null(cols_to_remove)){
jd <- jd %>% dplyr::select(!all_of(c(cols_to_remove)))
jd %<>% dplyr::mutate(used = if_else(is.na(used), FALSE, TRUE), .keep = "all")
jd %<>% dplyr::arrange(desc(used), well_row, well_col)
jd = jd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)))
class(jd) = c("mod_normfluodbf_data", class(jd))
jd
load_plate_data(plate) = jd
status(plate) = define_status(plate)[['MODIFY_DATA']]
steps(plate) = plate[['steps']][-1]
plate
}
else {
jd %<>% mutate(used = if_else(is.na(used), FALSE, TRUE), .keep = "all")
jd = jd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)))
class(jd) = c("mod_normfluodbf_data", class(jd))
jd
load_plate_data(plate) = jd
status(plate) = define_status(plate)[['MODIFY_DATA']]
steps(plate) = plate[['steps']][-1]
plate
}
}
#' @rdname modifyplatedata
#' @return plate
#' @export
modify_plate_data.1536well_plate_t1 = function(plate){
CURRENT_STEP <- plate %>% step('MODIFY_DATA')
cols_to_remove = 'sample'; bycol = "well"
jd <- dplyr::left_join(plate[['plate_meta']],
plate[['plate_data']],
suffix = c("",""), #can also use original vs new suffix
by = bycol
) #multiple = "all" for full joins
if(!is.null(cols_to_remove)){
jd <- jd %>% dplyr::select(!all_of(c(cols_to_remove)))
jd %<>% dplyr::mutate(used = if_else(is.na(used), FALSE, TRUE), .keep = "all")
jd %<>% dplyr::arrange(desc(used), well_row, well_col)
jd = jd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)))
class(jd) = c("mod_normfluodbf_data", class(jd))
jd
load_plate_data(plate) = jd
status(plate) = define_status(plate)[['MODIFY_DATA']]
steps(plate) = plate[['steps']][-1]
plate
}
else {
jd %<>% mutate(used = if_else(is.na(used), FALSE, TRUE), .keep = "all")
jd = jd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)))
class(jd) = c("mod_normfluodbf_data", class(jd))
jd
load_plate_data(plate) = jd
status(plate) = define_status(plate)[['MODIFY_DATA']]
steps(plate) = plate[['steps']][-1]
plate
}
}
#' @rdname modifyplatedata
#' @return plate
#' @export
modify_plate_data.1536well_plate_t2 = function(plate){
CURRENT_STEP <- plate %>% step('MODIFY_DATA')
cols_to_remove = 'sample'; bycol = "well"
jd <- dplyr::left_join(plate[['plate_meta']],
plate[['plate_data']],
suffix = c("",""), #can also use original vs new suffix
by = bycol
) #multiple = "all" for full joins
if(!is.null(cols_to_remove)){
jd <- jd %>% dplyr::select(!all_of(c(cols_to_remove)))
jd %<>% dplyr::mutate(used = if_else(is.na(used), FALSE, TRUE), .keep = "all")
jd %<>% dplyr::arrange(desc(used), well_row, well_col)
jd = jd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)))
class(jd) = c("mod_normfluodbf_data", class(jd))
jd
load_plate_data(plate) = jd
status(plate) = define_status(plate)[['MODIFY_DATA']]
steps(plate) = plate[['steps']][-1]
plate
}
else {
jd %<>% mutate(used = if_else(is.na(used), FALSE, TRUE), .keep = "all")
jd = jd %>%
dplyr::mutate("well_row" = gsub("[[:digit:]]", "", well),
"well_col" = as.factor(gsub("[^0-9.-]", "", well)))
class(jd) = c("mod_normfluodbf_data", class(jd))
jd
load_plate_data(plate) = jd
status(plate) = define_status(plate)[['MODIFY_DATA']]
steps(plate) = plate[['steps']][-1]
plate
}
}
#' Upload Plate Data
#' @family uploadplatedata
#' @param plate plate
#' @param file file
#' @param ... dots
#' @return plate
#' @name uploadplatedata
#' @examples
#' \dontrun{upload_data(plate, file, ...)}
NULL
#' @rdname uploadplatedata
#' @return plate
#' @export
upload_data <- function(plate, file, ...){
UseMethod("upload_data")
}
#' @rdname uploadplatedata
#' @return plate
#' @export
upload_data.default <- function(plate, file, ...){
CURRENT_STEP <- plate %>% step('DATA_INITIALIZED')
plate %>% check_step(CURRENT_STEP)
step_begin('Initializing Data')
pd = quiet({plate_data(file, ... )}, suppress_messages = T, suppress_warnings = T)
#plate[['persistent_data']] <- pd
wells_used = get_wells_used(pd)
load_plate_data(plate) = pd
plate = check_dirt(plate)
plate[['dirty']] <- TRUE
if (plate[['dirty']]){
status(plate) = define_status(plate)[['DATA_INITIALIZED']] #length(steps(plate)) - (length(steps(plate)) - 1)
steps(plate) = plate[['steps']][-1]
file_name_without_ext <- tools::file_path_sans_ext(basename(file))
plate[['dataset_name']] = file_name_without_ext
}
step_end('Data Initialized')
plate
}
#' @rdname uploadplatedata
#' @return plate
#' @export
upload_data.96well_plate <- function(plate, file, ...){
CURRENT_STEP <- plate %>% step('DATA_INITIALIZED')
plate %>% check_step(CURRENT_STEP)
step_begin('Initializing Data')
pd = quiet({plate_data(file, ... )}, suppress_messages = T, suppress_warnings = T)
#plate[['persistent_data']] <- pd
wells_used = get_wells_used(pd)
load_plate_data(plate) = pd
plate[['dirty']] <- TRUE
plate = check_dirt(plate)
if (plate[['dirty']]){
status(plate) = define_status(plate)[['DATA_INITIALIZED']]
steps(plate) = plate[['steps']][-1]
file_name_without_ext <- tools::file_path_sans_ext(basename(file))
plate[['dataset_name']] = file_name_without_ext
}
step_end('Data Initialized')
plate
}
#' @rdname uploadplatedata
#' @return plate
#' @export
upload_data.384well_plate <- function(plate, file, ...){
CURRENT_STEP <- plate %>% step('DATA_INITIALIZED')
plate %>% check_step(CURRENT_STEP)
step_begin('Initializing Data')
pd = quiet({plate_data(file, ... )}, suppress_messages = T, suppress_warnings = T)
#plate[['persistent_data']] <- pd
wells_used = get_wells_used(pd)
load_plate_data(plate) = pd
plate[['dirty']] <- TRUE
plate = check_dirt(plate)
if (plate[['dirty']]){
status(plate) = define_status(plate)[['DATA_INITIALIZED']]
steps(plate) = plate[['steps']][-1]
file_name_without_ext <- tools::file_path_sans_ext(basename(file))
plate[['dataset_name']] = file_name_without_ext
}
step_end('Data Initialized')
plate
}
#' @rdname uploadplatedata
#' @return plate
#' @export
upload_data.1536well_plate_t1 <- function(plate, file, ...){
CURRENT_STEP <- plate %>% step('DATA_INITIALIZED')
plate %>% check_step(CURRENT_STEP)
step_begin('Initializing Data')
pd = quiet({plate_data(file, ... )}, suppress_messages = T, suppress_warnings = T)
#plate[['persistent_data']] <- pd
wells_used = get_wells_used(pd)
load_plate_data(plate) = pd
plate[['dirty']] <- TRUE
plate = check_dirt(plate)
if (plate[['dirty']]){
status(plate) = define_status(plate)[['DATA_INITIALIZED']]
steps(plate) = plate[['steps']][-1]
file_name_without_ext <- tools::file_path_sans_ext(basename(file))
plate[['dataset_name']] = file_name_without_ext
}
step_end('Data Initialized')
plate
}
#' @rdname uploadplatedata
#' @return plate
#' @export
upload_data.1536well_plate_t2 <- function(plate, file, ...){
CURRENT_STEP <- plate %>% step('DATA_INITIALIZED')
plate %>% check_step(CURRENT_STEP)
step_begin('Initializing Data')
pd = quiet({plate_data(file, ... )}, suppress_messages = T, suppress_warnings = T)
#plate[['persistent_data']] <- pd
wells_used = get_wells_used(pd)
load_plate_data(plate) = pd
plate[['dirty']] <- TRUE
plate = check_dirt(plate)
if (plate[['dirty']]){
status(plate) = define_status(plate)[['DATA_INITIALIZED']]
steps(plate) = plate[['steps']][-1]
file_name_without_ext <- tools::file_path_sans_ext(basename(file))
plate[['dataset_name']] = file_name_without_ext
}
step_end('Data Initialized')
plate
}
#' Load Plate Data
#' @family loadplatedata
#' @param plate plate
#' @param value data
#' @return plate
#' @name loadplatedata
#' @examples
#' \dontrun{load_plate_data(plate,value = data)}
NULL
#' @rdname loadplatedata
#' @return plate
#' @export
load_plate_data = function(plate){
stopifnot(plate %>% inherits("normfluodbf_plate"))
plate[['plate_data']]
}
#' @rdname loadplatedata
#' @return plate
#' @export
`load_plate_data<-` <- function(plate, value) {
stopifnot(plate %>% inherits("normfluodbf_plate"))
plate[['plate_data']] <- value
plate
}
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